I conclude, that some expected data has been lost at some point in time.
Loosing data smells a bit to the file I opleaded where a point was dropped when adding seam allowance, but that can be coincidence also and be another bug.
Actually the dropped point is there twice (it's the upper right corner of the left part; it's also te upper right corner of the second part.)
Can't reproduce. Need correct instruction for reproducing.
I tried to further isolate it, but wasn't able to. Maybe it is as you said, that the file has been broken before the union operation, but it does only manifest during the union operation. For preparation i tried to delete all details in the xml file directly and reproduce the error, but with a clean xml-detail, it didn't reproduce. There is still some entropy in this. However as this has been a normal working file with a lot of previous operations done to it, including to the source xml file, chances are, it is the result of any sort of handling error.
Although not certain, I think probabilities are high, this is actually a user handling error and no bug.
Sorry for not being able to provide you a file for proper reproduction :/