When your 3PL's receiving count comes in below what you shipped, find where the units went before anyone adjusts a number: cartons first, then total units, then what's inside the cartons, then a recount. Each cause leaves a different record, and each one has a different party who pays.
Compare cartons on your packing list, the bill of lading and the signed delivery receipt before you compare units. Missing cartons point to the supplier or the carrier, and a carrier claim needs a written dollar amount (federal law allows no less than 9 months to file). If every carton arrived, check for wrong-SKU units, a wrong case pack, then a miscount.
What a receiving discrepancy looks like
A receiving discrepancy is any gap between the units you sent and the units your 3PL logs as received, short or over, by SKU. A thread on r/logistics from April 2026 is a clean case: a brand sent 500 units across two SKUs, counted and photographed before pickup, and the 3PL's dashboard showed 471. Five days later the 3PL was "still reconciling the inbound."
Twenty-nine units is 5.8% of that shipment. At a Shopify brand doing 1,000 to 10,000 orders a month, the same percentage on a 5,000-unit inbound is close to 300 units, and Shopify can only sell what the receipt says arrived.
Find the cause in this order
Work from the outside of the shipment in, so you don't spend a week arguing about a miscount when the carrier delivered 18 cartons instead of 20.
1. Count cartons against three documents
Line up the carton count on the supplier's packing list, the piece count on the bill of lading (BOL) and the piece count on the delivery receipt the warehouse signed. If the BOL already shows fewer cartons than the packing list, the supplier or the factory loaded short. If the BOL matches the packing list but the delivery receipt notes fewer pieces, the carrier lost them. At our dock, receiving has arrival photos, so the carton count and condition at delivery are on record before anything is opened.
A delivery receipt signed clean, with no shortage noted, is the hard case. PITT OHIO tells consignees to verify the piece count against the delivery receipt while freight is unloaded and to note any shortage in specific terms, and it requires concealed damage to be reported within 48 hours of delivery. Other carriers set their own notice periods, so a short count needs to reach you fast.
2. Add up every SKU before you call it a loss
If all cartons arrived, total the received units across every SKU on the receipt and compare that with the packing list total. When the total matches but one SKU is short and another is over, nothing is missing. Units went in under the wrong SKU, usually because two products share a carton label or a barcode was scanned off the wrong item.
Check units held outside sellable stock too. A Shopify oral care brand moving to us sold a Complete set and a Duo set, but only the brush had a SKU. Before receiving, we asked for a SKU or barcode and a weight on every product, and units that arrived before setup were held until the products were in the system. Held units don't show as available in Shopify, so a brand that only looks at Shopify sees a shortage.
3. Open sealed cartons and check the case pack
If the total units are short and every carton arrived, open a sample of sealed cartons and count them against the carton label. A carton labeled 24 that holds 20 is a supplier packing error. A count that is short by an exact ratio, such as one sixth of the expected units, points to a unit-of-measure error: inner packs counted as single units, or a case quantity set wrong in the product record. Carton weights help here, because a short carton weighs less than its siblings.
4. Ask for a recount, then a written variance
Only when the cartons, the SKU totals and the case packs all check out is a 3PL miscount the likely cause. Ask for a recount of the affected SKUs, by someone other than the original counter, and a variance by SKU: expected, received, damaged and the difference.
What an overage means
An over count on one SKU almost always sits next to a short count on another, so treat it as a mapping error until the SKU totals prove otherwise. A true supplier overship still needs a note on the receipt, or your landed cost won't match the invoice.
Who pays for each cause
The party responsible at the handoff where the units went missing pays, and the record from that handoff decides it.
| Cause | What you'll see | Evidence that settles it | Who pays |
|---|---|---|---|
| Supplier short-ship | BOL carton count matches the delivery, but below the packing list, or sealed cartons short inside | Packing list, BOL piece count, photos of sealed cartons, carton weights | Supplier, by credit or replacement |
| Carrier loss or damage | Delivery receipt notes fewer pieces or damage, or damage found after unloading | BOL and delivery receipt with exceptions, arrival photos, freight invoice | Carrier, through a written freight claim |
| Case-pack or unit-of-measure error | Units short by an exact multiple, every carton present | Carton label against a counted sample, product record case quantity | Supplier for a packing error; nobody for a data error, which is a correction |
| SKU or barcode mapping | One SKU short, another over, or units held as unidentified | SKU totals against the packing list, list of held units | Nobody; the 3PL moves units to the right SKU |
| 3PL miscount | Cartons, totals and case packs check out | Blind recount, receiving variance by SKU | The 3PL, under the contract's liability terms |
How carrier claims work
A freight claim has to be written, tied to the shipment and for a specific amount. Under 49 CFR 370.3, a shortage noted on a delivery receipt does not count as a claim on its own. The carrier must acknowledge a claim within 30 days (370.5) and pay, decline or make a firm settlement offer within 120 days (370.9).
49 U.S.C. 14706(e) bars motor carriers from setting less than 9 months to file a claim, or less than 2 years to sue after a written denial. PITT OHIO cites Section 3(b) of the Uniform Straight Bill of Lading for its nine months from delivery. Parcel inbound runs on shorter clocks: FedEx wants claims for damaged or missing contents within 60 calendar days of the shipment date for US packages. Attach the supplier invoice for value, the BOL, the delivery receipt and your photos, and have a lawyer handle a claim the carrier denies.
What an unresolved short count costs at your volume
The units in dispute are the smaller part of the cost. A short receipt lowers what Shopify can sell, and the reorder plan you built on the PO quantity is wrong from that day.
Example, not Orderfy rates: a brand at 6,000 orders a month whose hero SKU sells 80 units a day sends 4,800 units of it, and the receipt shows 4,440.
| Line | Example figure |
|---|---|
| Units short | 360 |
| Days of stock lost (360 ÷ 80 a day) | 4.5 days |
| Sales at risk if you stock out before the next PO lands ($38 price) | $13,680 |
| Contribution at risk ($20 a unit after landed cost, fulfillment and postage) | $7,200 |
| Inventory value in dispute ($9 landed cost) | $3,240 |
The reorder date moves too. If the 360 units are truly missing, your reorder point arrives 4.5 days earlier than the PO plan said, and with a 45-day supplier lead time a late reorder means a stockout. If the units are sitting under another SKU, you reorder early and pay to store stock you already own. The reorder point guide covers safety stock, and stopping overselling covers count gaps in Shopify.
The sooner the count is done, the more of these options you still have. We receive within 24 hours of delivery, and received inventory typically takes less than 1 business day to reach sellable stock. A count finished that soon lands inside the shorter carrier notice periods, such as PITT OHIO's 48 hours for concealed damage.
Shrink allowances don't cover a receiving count
Google's AI Overview for this query says 3PL contracts typically allow 1% to 2% shrinkage on an initial inbound. The contracts we checked measure shrink over a year of inventory in the warehouse's care, not on one delivery. Stord's Warehouse Terms (effective February 14, 2026) set a 0.5% allowance calculated on a rolling 12-month basis, and Flexport says it isn't liable for shrinkage up to 1.5% of inventory value on an annual basis.
A receiving clause should say something different: the 3PL counts each inbound against the advance shipping notice (ASN) by SKU, reports any variance by SKU with arrival photos, and doesn't adjust your stock until the cause is found. The contract negotiation guide covers liability caps and notice windows, and the SLA metrics guide covers dock-to-stock targets.
What to send before the next inbound
Send these with every inbound, so each carton can be checked against an expected quantity:
- An ASN or packing list with the carton count, units per carton and total units for each SKU.
- A SKU and scannable barcode on every carton, and on every unit you sell on its own.
- Product records set up first: SKU or barcode, weight and the contents of every set or bundle.
- A BOL with the piece count, signed by the driver at pickup, and photos of the loaded cartons.
A Shopify oral care brand's Q4 inbound was about 5,000 units across brushes, tongue scrapers and travel cases, and we received it against an advance shipping notice, so every SKU had an expected quantity before the first carton was opened. The 3PL onboarding checklist lists the full set of data a warehouse needs before your first delivery.
How we receive an inbound
We receive within 24 hours of delivery, and received inventory typically takes less than 1 business day to reach sellable stock. Our receiving records include arrival photos. Units that arrive before their products are set up are held until they're in Orderfy WMS, the proprietary inventory software we built in-house for Shopify and Amazon sellers, and received stock syncs to Shopify in real time.
Frequently asked questions
Check cartons against the packing list, BOL and delivery receipt first, then total units across SKUs, then case packs, then ask for a recount. Each step points to a different party, and the record from that handoff decides who pays.
A delivery discrepancy is a gap between what the bill of lading says was shipped and what arrived: missing cartons, extra cartons or damage. Note it on the delivery receipt at the dock, then file a written claim, because the notation alone isn't a claim under 49 CFR 370.3.
Long enough to finish the count, and well inside the carrier's notice period. A concealed loss reported after the carrier's deadline (48 hours at PITT OHIO) is much harder to recover, so a reconciliation that takes a week costs you the claim.
Send your next inbound to a team that counts it fast
Request a quote and we'll walk through how your next inbound is received and synced to Shopify.
Sources
- 49 U.S.C. 14706, Liability of carriers under receipts and bills of lading, checked November 8, 2026
- 49 CFR Part 370, Investigation and voluntary disposition of loss and damage claims, eCFR up to date as of November 5, 2026, checked November 8, 2026
- PITT OHIO, LTL claims, checked November 8, 2026
- FedEx, claims, checked November 8, 2026
- Stord Warehouse Terms, effective February 14, 2026, checked November 8, 2026
- Flexport Help Center, What is the Inventory Shrinkage Allowance?, checked November 8, 2026
- Reddit r/logistics, "Sent 500 units to a 3PL for the first time and the inventory count in their system doesn't match what I shipped", April 14, 2026