I upgraded to the latest version of Stellarium about a month ago, and one it's "features" drives me nuts. It seems to insist upon displaying the horizon of various locations around the world. This horizon of course blocks the view of anything behind it. What a bonus! I was finally able to get my preferences to stick so that when I fire up the application there is no weird horizon masking things out. It initially only allowed me to change to no horizon mask for one session of the app. Quit the app and the weird horizon returned upon firing up the app again. Now if they allowed me to create a mask for my own backyard, with my local obstructions, now that would be something...

What's your favorite "bonus feature" of some application that bugs you?

iTunes in total. It's like Apple took all the incompetent interface designers, didn't allow them to read the human interface guidelines, and turned them loose with QA handled by a group in northern China.

They probably did.