To remove plays from the website:

On the website, click a watched check mark again and you’ll get a prompt confirming you want to remove all plays for that item. 

Remove individual plays from your history page. Just click the check mark and there will be an option to only remove the single play.

To remove plays from the official Trakt App for iOS:

In the app, on a movie or episode listing, you can click the right section of the red Track button with the history icon to see all your plays for that episode or movie.  You can click Remove All in the upper right corner of the history page, or swipe left to delete an individual play.  

You can also view your watched history of the entire show by clicking on the down triangle on the right side of purple Progress/Watched button and then selecting View Full Watch History.  

To see your entire watched history, from the home screen of the app, scroll down to the Recently Watched section and click See All.  To remove an individual play, swipe left on it.