Same situation but after studying the issue for awhile it became clear after seeing the overages and under counts (both happen), things seem to balance themselves out and the overages get very close or exactly even with the undercounts, almost like Amazon is correcting itself whilst putting the blame on us for shipping more than we said we did which we didn’t.
We will send in a full pallet (maxed out on height) of 6000 units and sometimes Amazon will say they got 6048 (2 extra case packs), when the last shipment was checked in 48 units short.
It’s bizarre. We never made a big deal about this because of our low COGs and was saving up reimbursement requests for when things really matter like lost full shippers or pallets.