FT resident of MA, trouble w/ filing taxes in MA + CA

Hello. I am a full-time resident of MA but I work remotely for a company in CA. I am filing as a nonresident for CA and resident for MA.  As I am going through my taxes these two things have come to my attention.

  • I had CA taxes deducted from my paychecks, and the tax software I'm using is projecting a CA tax return of approx $500
  • I have to pay MA extra taxes ($1400ish) because of the CA work I did while physically being in MA 

I am pretty confused. I recently learned that MA will tax my CA income b/c I was physically in MA while helping this CA company. And that I should NOT be paying taxes to CA even though it's been automatically deducted from my paycheck. Does this mean I can ask my employer for an amended W-2 form where the CA tax is not deducted from my paychecks? 

 

Sorry if this makes no sense.