This is actually by design. The watchlist is a special “I want to watch” list for you to remember to watch something. Once you watch it, it automatically gets removed. The play is added to your history.
In the case of shows, once you watch 1 episode, the site will update and the show will continue showing up on your personal calendar, your continue watching view while there are more episodes to watch, and your progress view otherwise. So, there is no need to keep it on the watchlist. If you need to keep something around, you can always make your own custom list.
If you have any other questions about the watchlist in general, please read this: What is the Watchlist? What kind of items should I add to it? - Support / Tutorials - Trakt Forums