Are they authorized within Trakt? Trakt might be having issues. Check on the site see if it is in fact marked as watched. It could be marked on the site and just waiting to perform the watched status update on Kodi.
You could also run the Trakt addon see if it marks them as watched.
well that didn't work for me on the trakt install, this all started when the only info I was Seeing was the "CDATA" stuff, I have been using leia 18.3 since it auto upgraded, I'm going to tinker with it some more, One more time, HOW DO I CHECK OFF EPISODES OR MOVIES WATCHED ?
I stayed with trying to load Trakts and adding tv show tracker, Mission accomplished, but I had to jump through and over many obstacles. I would prefer the check off system, I keep thinking it was Ex**us Redux that caused the problems for me, ????
RavBob it has taken me till today, Jan 18th to get my "Watched Episode" check mark back, it was as you said a DEV issue, I started looking at FEN as suggested by another commenter , I didn't like TRAKT because it was just an extra step and also another program to take up valuable space on my box and computer, Thank You