To me this sounds like the xochitl application (aka "the reMarkable UI", the software you're actually using on the tablet) has ...
- an in-memory list of which tags are attached to which documents or pages
- a function which updates or rebuilds this list "as needed"
... and it sounds like that update function isn't being called in every case where tags may be added or updated.
In other words, it sounds like a bug in the reMarkable software. (My $DAYJOB involves software development, I deal with troubleshooting, identifying, and fixing bugs on a very regular basis.) (When I'm not on vacation, which I have been since last week.)
I would recommend contacting reMarkable support about this. You probably won't get an immediate solution (other than "restart the tablet" whenever you find that the list is incorrect, which it sounds like you've already been doing) but it will at least put the bug on their list of problems needing to be fixed, and hopefully a future version of the software will contain a fix for it. (And the fix will probably only described as "bug fixes and updates", since most companies don't seem to like detailing the actual bugs they're fixing.)