Are you filing the states as Married filing Separate?
If you need to file a Joint federal and separate state returns
https://ttlc.intuit.com/community/using-turbotax/help/how-do-i-prepare-a-joint-federal-return-and-se...
You have to use 3 different new returns. One to file the Joint return. Then you each need another new return to fill out fake federal MFS returns to do your separate state returns. You will have to print and mail the state returns.
