We ran into an issue where 2 branches decided to create a label batch around the same time. Both had the blank batch screen up and they were the same batch number. We have found that the batch isn't actually committed as being used until the first item is added. In this case we had 2 branches adding items to the same batch number. This can be duplicated by creating a new batch in 2 separate browsers. If party 2 refreshes the screen after party 1 enters an item to the batch they are presented with a new batch but if they don't refresh (which most wouldn't) then both parties are editing the same batch. We have tested it in 3.6 and 3.8.
Until this problem is fixed one workaround is to click the Add Item button as soon as the very first barcode has been scanned. This way Koha will assign a new batch number. The rest of the barcodes can then be scanned. It's not a perfect solution but should reduce the chances of barcodes from multiple libraries ending up in the same batch.
I believe this is the same problem as bug 12911 - marking them duplicate so discussion can continue on one report. *** This bug has been marked as a duplicate of bug 12911 ***