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@cmcgeehen wrote:

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.

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What do you mean they were nonresidents moving from MA to CT in 2018?  I suppose you are amended the 2018 return and that would make them both PY and NR for MA tax purposes, not nonresidents.

Also, MA (although a tough state to break domicile with) has a very straight forward tax regime which assesses 5.1% on most categories of income other than capital gains, which is subject to a 12% tax.  It is not clear how filing MFS would benefit them just because one spouse earned the income in NJ and CT as a credit would then be claimed for the portion earned during the PY period on the MA return.

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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. 

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It is not clear what you are proposing to do.  But MA does require both spouses' income to be combined only if they file jointly.  However, this should have no material tax effect on PY/NR filers.  The inclusion of the other spouse's income will affect the proration of exemption (the numerator of which is only MA source income) that could be applied against the 5.1% income but only if they were NR, which they were not, based on what you stated.  For PY, the proration is based on day-count for the resident period instead.

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@cmcgeehen wrote:

I don't think the system allows the returns to be split. I will most likely have to efile federal and then file MA on paper. 

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Even if you decide to file MFS, the reason of which is not clear, the MFS returns for both spouses can still be e-filed because MA is a Standalone state.  There is no need to file the returns on paper (at least for the original 2019 returns).

[Edit: Added comments about paper filing for 2019 and to clarify inclusion of spouse's income]