The following answer assumes that you have a health FSA and not a limited purpose FSA, such as for vision only or for dependent care coverage. If you have a limited FSA, please tell us in the comments what type it is.
First, was your spouse covered by your FSA? If so, as it looks like you know, she was not eligible to make contributions to her HSA.
When you go through the HSA interview (Federal->Deductions & Credits->Medical->HSA MSA Contributions), when you are asked about her HDHP coverage ("Was [name] covered by a High Deductible Health Plan (HDHP) in 2017?"), answer "No, I did not have coverage." (The HDHP coverage was negated by the FSA coverage).
This will cause all of her contributions in 2017 to be declared "excess". TurboTax will next ask if you want to withdraw the excess before the due date of the return (April 17th). If you have the money, answer "yes".
Contact your HSA administrator and tell them you want to withdraw an "excess contribution" made in 2017. They will send you a check for that amount from your HSA.
As soon as TurboTax detects the excess, it will add that amount to line 21 (Other Income) on your 1040. You don't have to do anything else.
If you cannot withdraw the entire amount from the HSA (because you don't have enough funds), withdraw as much as you can; the rest will carry over to 2018 and be assessed a 6% penalty. This 6% penalty will carry over until your spouse is no longer covered by your FSA (i.e., she can start to contribute to her HSA again) and the excess is charged off against a future annual contribution limit, or until she takes a distribution for non-medical expenses which will cost her not only income tax on the distribution but also a 20% penalty unless she is 65 or older.
My recollection is that a health FSA automatically covers the spouse, so you need to have a sit-down with your benefits co-ordinator and her benefits co-ordinator and decide which plan you are going to go with.
