Interesting, I have never seen that happen. Are you sure you are not experiencing a Z-order problem, where content is not altered but the reading order is changed such that certain content elements are hiding behind others?
Hmm I've never heard of z-order so I'm not sure what that is, but even if it is just a reading order change I would think it should still keep the text in the same place on the PDF. (silly me?)
We don't do a lot of manual tagging or touch ups but will this fix the problem?
My description and video of the Z-order problem is here https://taggedpdf.com/508-pdf-help-center/z-order-problem/
Google can of course find other descriptions and suggestions.
Manual tagging is certainly worth a try anytime auto-tagging does not produce satisfactory results.