We're using an autonumber in an entity to generate a barcode. It seems that this autonumber has been reset, because we're seeing double numbers in our barcodes. We migrated our app in from 2.5 to 3.3 in august 2012. How can it be that the autonumber has been reset? Edit after comment: How does the autonumber technically work? It's not the same as the id of the object.
That seems pretty much impossible to answer with so little information. I suggest trying to reproduce this with your old 2.5 database and project and filing a ticket if you can.