Ok, while not having seen it recently, I'll give it a try based more on common sense than exact information from the respective episodes. While I don't exactly remember if or when she definitely finds out, the fact that she "numerously indicates that Brody is sleeping with the CIA girl" doesn't necessarily imply that she really finds this out.
Even if not exactly knowing that Brody had (yet again) an affair with Carrie, she had all the reasons for suspecting it. She already knew back from the 1st season (and back then she definitely knew, however I don't remember how) that Brody once had an affair with Carrie and it was a major problem for their whole relationship (together with other things, though).
So when she now comes to know that he is working for the CIA again, and later maybe (though I don't remember exactly) even comes to know that he works exactly with Carrie albeit having claimed not to at first, paired with his generally suspicious behaviour, she naturally mistrusts him. So given his past history, their difficult relationship, his suspicious behaviour, his little lies, his job-related proximity to Carrie, and a bit of a wife's natural jealousy, I don't think she needs a definite proof for assuming an affair between Brody and Carrie.