Yes... you are correct. The system won't allow it. 

Spouse earned $22k in MA and together they earned over $400k. They are non residents moving from MA to CT in 2018.  My client's former CPA filed her MA separately since all of the spouse's income has always been earned in NJ & CT. But she incorrectly filed her MA as a single taxpayer and didn't include their total income as part of the MA pro-ration calculation which is what I think you are supposed to do when filing MFS so my client thinks I am doing it wrong. MA instructions only say that federal total and AGI need to be combined on the MA MFS return but does not also indicate whether the total income from all sources outside of MA need to be combined for the MA return as well. I think it does but client is disagreeing with me... because of prior year CPA I guess.