This seems to be pretty rare. I’m sorry it happened to you. Of the two reports I could find, this was also AV damage, though I don’t know why AV damage would be anything special. Regardless, it had a workaround:
When on your Database page, instead of simply doing Recreate you could consider making a copy of the database beforehand just in case something goes wrong in the Recreate and we want to try old DB again.
Maybe a Repair would help, but it’s never clear what Repair can fix, and it sometimes harms destination. Recreate doesn’t always work well, but at least it doesn’t change the destination (the actual backup data).
You could also post a DB bug report so someone can maybe make some sense of its damage, but it’s not guaranteed that will be possible, and it probably also won’t lead directly to knowing how things got that way.
To benefit anybody following this chase, I think this is the detection code. There’s one table listing files. File may appear multiple times if different versions exist. Each of them should be in a different table organized by backup version (which contains files). In this case, some files did not have a containing backup version.