How does sharingan see through genjutsu at all? For genjutsu to be cancelled, the genjutsu castor's control of the victims chakra has to be overpowered by stopping the flow of chakra. The victims chakra can't be irregular, we see that this is the same regardless of whether or not the victim has a sharingan, because Karin mentioned Sasuke wasn't in a genjutsu. She figured this out, because Sasuke chakra flow wasn't irregular.
Well, to be honest, there are other types of genjutsu that can easily be figured out as one, but still be unable to be countered with. Like Jiraya's and the Sound Ninja's genjutsu, which captyres the person, and even though they know they're in it, they are stuck. And just like that, there is the Sharingan Genjutsu which kind of treats the opponents into mental pain that is felt physically or something, like the Tsukuyomi and the genjutsu Sasuke did with C and Sakura. And then, there is the controlling one. Which kind of works with target being unconscious of whatever he or she is doing, like with Kurama, Manda, and many other examples.