MO will require the same filing status to be used as the federal return while your clients seem to qualify under an exception to use MFS for the NE return.

What this means is that the spouse's NE income will be reportable and taxable on the MO return (See instructions for MO-1040, Line 1).  Other state tax credit would then be claimed on the MO return for NE tax.

You should be able to e-file the NE MFS return since NE permits state only e-filing: https://proconnect.intuit.com/support/en-us/help-article/electronic-filing/state-e-file-methods-stan...