Uncomfortable can mean anything, scary, sad, creepy, gory etc...
I was just watching AHS this afternoon, the Cult season and there is a scene with a nail gun (if you've seen it you'll know!).
I am really not a squeamish person but this scene just made me go cold, I was about to fast forward it before it finished.
It wasn't even the most gruesome thing I've seen on TV/a movie before but the whole idea just made me feel really uncomfortable and like I was really horrible for watching it if that makes sense?