There are three primary causes:

1. Stock in archived locations

2. Stock for archived products

3. Automatic valuation was enabled when items were in stock

You will typically only see this error when using automatic inventory valuation. This is because in auto valuation, the valuation report is built using account.move.line records where product=product, account=product's valuation account. The quantity and value of each move is used to compute the report value. 

Items 1 and 2 are a problem because: Stock in these conditions is hidden from reports built using stock move but not from accounting. In other words, you've hidden the stock quantities but the ledger impact remains. You should have written off all value of a product before you archived it and written off or moved all stock out of a location before you archived it.

You can correct the issue by unarchiving the locations/products, removing their stock, and then rearchiving.

Item 3 is a problem because the stock and account move records are discontinuous. Accounting entries do not exist corresponding to some stock moves, obviously resulting in a discrepancy.

You can fix the issue by backfilling the missing journal entries. When creating these backfilled entries, be sure to pick the correct product, account, quantity, and value. A negative quantity on an account move deducts quantity while a positive quantity adds it (from the perspective of the valuation report).