If you’re on the new beta server 1.40 there was a change to how manually marking items as “watched” was recorded: Plex Media Server - #609 by drzoidberg33
There’s a thread on it a bit too: View History Change in 1.40.0.x server version
That seems like it might be related here.
Essentially, if you mark was watched manually, it isn’t treated as “actually watched”, it just removes the watched status without creating a historical entry for it unless you actually watch it through. Personally I like that change but it could throw off other things like trying to clear a watch list just by marking it as watched - you’d have to click “remove from watchlist” instead now.