My problem, which has been going on for over a week now, is basically the same as the one documented here Episodes not marked as watched only attempting to reset the cache is not working because the process is taking many hours with no end in sight.
Where did you mark those episodes as watched? Do they show up in your history?
Can you please sign out of Trakt, clear the Trakt web browser cookies, and sign back in. Then check if it works after doing this?
Both on an app and on the webpage?
How are you watching/scrobbling?
(Figure these are the first two questions @support would ask)
EDIT: I was close! 
Support replied the same time I did.
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Yeah… Signing out and clearing cache did not work.
Shows up on history but episode itself is not marked as watched. Tends to happen every so often.
Opened episode straight from Watched History, but…
Did you mark those episodes in the app? In the website? In the lite version? Using a scrobbler? Using a third party app?
How did you mark those episodes?
Don’t really use the app, but most recent episodes were marked by the scrobbler
I mostly marked episodes as watched using the website, others I marked using the Trakt app. This problem appears on both PC and android and in multiple browsers but not on the app.
Just making sure you know you now have two different people you are troubleshooting for. I was about to reply to one and realized it was someone else
Yes, I noticed.
I’ll ask the developers what else can be done.
i have a support ticket pending with this exact same issue, i have provided screenshots of the console and network tabs also. it seems that the json file that has watched data is getting a 500 error when trying to be accessed. weird thing is that when i did a data export the episode json downloaded absolutely fine.
glad its not just me that it having the issue though, although also not glad that anyone is getting the issue 
Same same. There’s at least one other thread in the forums with another experiencing the same issue.