You have only one "X" button to remove a torrent. I can't count the number of times that a torrent that was done was highlighted, I pressed the "X" button and a torrent that was sill working and was also highlighted (but not seen because it was not in the window) was removed instead. This has literally happened to me 20 times or more since I started using Azureus years ago. i try yo remember to always make sure that only one item is highlighted but sometimes there is one in each window, you can't see one of them and you forget. The working torrent gets deleted and then I have to jump through hoops to figure out which one it was.
What you need are two different "X" buttons. One to remove torrents that are completed and one to remove torrents that are not completed.
Have many other people found this to be a problem, also?