I can't get my state taxes correct. We both live in MA, her income is from MA mine is from CT. When I try to file CT taxes they are taxing us on our total gross income

When you have a nonresident and a resident return, it is important that you first complete the nonresident return. Delete both states and start again with the Connecticut return first.  What program are you using so I can help you with deleting the state?

There is a credit in Massachusetts that may benefit you:

If you earned income in another state while a resident of Massachusetts and both the other state and MA taxed the income, you can claim a credit for the taxes paid to the other state on your MA resident return. You must file a tax return in the other state. If you file a resident MA return and a nonresident return for the other state, the program will calculate the credit for you.

[Edited 03.25.19|5:39pm PST]