They are non residents for MA in 2019. They moved to CT from MA in 2018.  She worked for a hospital located in MA in both years. In 2019, she earned only $22k for that job and then opened her own practice in CT with a small loss in 2019. Her husband works for a hospital in CT and worked there all year. His income was all CT and totaled around $400k for 2019. She had the MA income of $22k and then her loss of $11k in CT for her own practice she started in 2019. 

The pro-ration is coming into the equation since her MA return is all NR for 2019. The system is taking all non MA income of $395k and taking the $22k earned in MA as a % of the total income as the pro-ration factor to apply against her exemptions. This is the dispute. Thus, her exemptions for her and her 2 children are being calculated at roughly 5.5% to deduct from the $22k income which is yielding a small amount owed.