As a full-time student, graduate stipends are exempt from FICA.
If her stipend amount didn't change and her W-4 exemptions didn't change, the withholding shouldn't have either, they should just use the standard formula. Go to paycheckcity.com and see what their calculation is.
Typically, any stipend that goes towards student health insurance is taxable - so pay attention to that.
Graduate student tax rules are complicated and the University is generally prohibited from providing tax advice, which is why it is hard to find any resources. There may be a VITA chapter at your wife's University, they may be able to help, but my experience was they were not very good at one student/one full-time worker married couple issues, especially if the spouse was an above median income earner.
It looks like this isn't the first year, so hopefully it's not all unfamiliar territory at this point. My wife also graduated this year after 6 years, and I think by last year, I finally had it all figured out, though her income mix, and mine, was different every year.
