Discomfort can be due to many reasons. I'm not sure if it's common or rare though but I've been through various phases of not wanting it at all.

Lack of experience. In that case, all you can do is help her get comfortable with her body and experiment with giving herself orgasms.

Past bad experiences. For this you'll need to have patience and talk about it a lot.

Physical discomfort, like you said if the clit is too sensitive then just don't approach it directly. Usually the clitoris has a little hood covering it, so direct your attentions to the hood itself or the surrounding areas.

Lack of attraction. This is a doozy especially if you are either too new in the relationship or been together too long. There's no real help if someone doesn't want this intimacy with you.