As far as I can tell, this only happens with one TV series. It has four seasons. Let’s start with the initial status quo of all episodes of all seasons are unwatched.
If I go to any season and either a) select the entire season, or b) go inside the same season and start selecting individual seasons (even a random selection), and mark them as WATCHED, it also affects random episodes in the other remaining seasons.
For instance, if I have 24, 24, 24, 24 as unwatched, select Season 1 and mark it as WATCHED, I might get something like the following: 0, 21, 23, 22. If I go to the incorrect seasons (say Season 3) and try to correct it (either by entire seasons or individually), I might get the following 4, 22, 24, 21.
In essence, whenever I start switching WATCHED/UNWATCHED, if affects the numbers in seasons not selected.
A couple of side notes: 1) The series was created in my early years when the encoding software would seem to randomly choose between mp4 and m4v. That’s the reason for the differences. (updates and me being more organized through experience has changed that), 2) I have watched this series in its entirety on multiple occasions previously with no problems, and 3) this behavior was noticed within past few days, and I’ve been on this server version since shortly after its release.