What can be done if my wife has an F1 visa but we found out that she was out of status before?

If your wife disclosed all the relevant facts regarding her previous E-2 status when she applied for F1 and, if the F-1 visa was not granted improvidently, then, she might be fine. But just on the outside chance this is not so, you may opt not to file her green card application until when she becomes a US citizen, particularly since she is still in the US on a valid F1 visa. Once you become a US citizen, then, you can file for her green card at that time. Most grounds of inadmissibility are waived for spouses of US citizens.

There is a chance that USCIS will not notice the out-of-status period in your wife's past. If they do raise this issue, there are arguments that might still win the case. But odds of either scenario are rather slim. I would advise you to hold off filing I-130 petition for your wife until you become a U.S. citizen. It will not guarantee an easy case (USCIS might argue that your wife's re-entry on an F1 visa was not a legal entry because she was inadmissible at the time, that she procured the visa by concealing her inadmissibility from the consul, etc.), but it will significantly increase the chances of winning it in the end. If you file I-130 after 2 years of marriage, it will lessen the USCIS scrutiny and eliminate the expenses and the hassle of going through the procedure of a conditional, 2-years green card, and of removal of conditions.

If she was out of status and remained in the US unlawfully for more than 6 months prior to returning to her home country, she may be required to file an I-601 waiver for unlawful presence.