Hi, I took my cat to the vet last week because she was acting weird and found out she had the flu, she is finally starting to feel better and act like herself again but her left eye is a bit cross eyed (which wasn't the case before) and her pupils are different sizes. I don't know if this is that I should be worried about or not. The white of her eye is also showing a lot more than it usually does. Does anyone know what could have happened? I don't know if it was a stroke or not, but I was reading all of the other symptoms and they don't seem to match.

It could be. It does sound like it.

The flu, huh? That's interesting.
Let me ask you this, how are her ears? Does she shake her head, scratch her ears? Has she had ear mites or past ear infections? Did they clean her ears while she was there?

The symptoms you are describing are a little vague right now, but check out the description of Horner's syndrome in cats:
Horner's Syndrome in Cats (http://www.peteducation.com/article.cfm?cls=1&cat=1344&articleid=2477)

Does this sound like your cat?
If it does, there is usually no need for treatment. We usually just wait for the symptoms to resolve on their own.
If not, give me a more detailed description of her prior illness (what brought her to the vet in the first place) and what she is doing now.