Sci fi gives us an amazing opportunity to look at ourselves through alien eyes. Who can forget the computer voice from Star Trek TNG’s Home Soil describing humans as Ugly bags of mostly water? It’s an accurate description (well, ugly is a matter of opinion).
Many aliens have described us as inferior and plenty have commented on our looks. Being able to distance oneself from our own race and discuss things that are obvious, is a privilege of the sci fi author.
In the short story collection The Cyberaid (by Stanislaw Lem) the robots call humans palefaces and think they are the most hideous beings in the universe.
If I remember correctly it was in Stephen King’s I Am The Doorway that an astronaut was infected by aliens and eyes grew on his fingers. These eyes saw humans as disgusting monsters.
Of course these are the literal interpretations but we have a very good recent example of humans being "ugly" in a less literal sense: the hugely popular movie Avatar. A lot of people were actually depressed after seeing that movie and frankly, I’m not surprised. It painted a rather disgusting picture of humans and, as I said before, that’s the privilege of the sci fi author :-)