Are you using LIFO or FIFO? Can you tell whether costing lots were emptied by shipments or adjustments or stock transfers? Could receipts for 0 qty and cost have been posted?
How do you ship stock, via Order Entry, Adagio Invoices or IC shipments?

When a costing lot is emptied by shipment, it should be deleted. All remaining lots should get 'moved up' when appropriate (ie FIFO). Certainly OE Day End processing does this after an item has been shipped It is possible that posting shipments directly in IC does not.

If a costing lot is emptied by adjustments, IC81B will leave the receipt number and date, even if the qty and cost are both reduced to zero. This may be what is happening to you.