Yes, any income derived from Massachusetts sources would be considered 'MA source income' and reported on a Non-Resident return. If you sold employee stock from a MA employer and received a 1099-B, any capital gain/loss would be reported on your non-resident return. Here's more info from MA Dept. of Revenue.
For a 'disqualifying disposition', add the amount from your W-2 (may be in Box 14) to the cost of the shares to get your correct Cost Basis. You can then enter the 1099-B as a regular stock sale (not employee stock).
Here's more detailed info on Employee Stock Purchase Plans.
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