There are 3 ways I know of that this can happen. One would involve more than one person adding a copy to the system at the same time. I don't think that's happening. Another way would be if you have items with all numeric barcodes already in the system whose numbers weren't made by the automatic barcode feature. A third way would be if you've entered more than about 10,000 items and your automatic barcodes no longer have leading zeros.
If none of these sounds like you, then I don't know what's causing your problem, and I'd really like to find out.
If one of the last two does sound like you, here's what you can do. Edit catalog/biblio_copy_new.php and find the line that looks like this:
Yes, I entered some barcodes just like OpenBiblio creates. But what should I edit? (I'm a beginner and / or the instruction is missing from your post :)
If most of the barcodes for your bibliography copies are made by the automatic feature, then I suggest that you try to correct the barcodes you've entered manually.
For understanding the barcode numbering structure, refer to OpenBiblio Help section 4b: Copy new and edit pages, subsection Barcode Number - Autogenerate.
Perhaps the Copy Search Report, sorted by barcode number, is useful for checking which barcode numbers do not correspond to the internal numbering structure. Following a link in the title column takes you to Bibliography Information / Bibliography Copy Information. From there, use the edit link to access the Edit Copy page. To correct a barcode number, use the values for bibid and copyid in the the browser location bar. As explained in Help, bibid needs to be entered with leading zeros.
In 0.6 autogenerating barcodes is implemented for New Copy only. For correcting problems like described in this issue, it would be helpful if Edit Copy also has an autogenerate option.
I've implemented this in my forked repository https://bitbucket.org/jgvdweij/obiblio,
changeset f8f6a64c02eb and 065b4102f7db