She has to file three state tax returns. She files a non-resident CA return and pays tax on the income she earned there. She files a non-resident NY return and pays tax on the income she earned there. She files a resident MA return and calculates tax on all her income for the year. But she gets a credit (maybe only a partial credit) for the tax paid to the other two states. Do the non resident returns first.
This is the general rule: The income is work state (WS) source income since it was earned there. Resident States (RS) tax all their resident's income, regardless of where earned. You will file a non-resident tax return for the WS and report the WS income. You will file a full year resident return for the RS, reporting all your income. The RS will give you a credit, or partial credit for any tax paid to the WS.
For state filing requirements, the WS does not, usually, go by what you earned in their state but by your total income . For example, if WS has a $10,000 filing requirement and your total income for the year was $15,000; you would be required to file even though you may have had only had $300 of income in that state. But if your total income was $9,000 you would not need to file.
Filing Requirements: https://ttlc.intuit.com/questions/2903200-do-i-need-to-file-a-state-return
