State tax filing

I recreated a scenario like yours, with $100,000 in wages, and the same $100K listed on my W-2 for both MA and RI. When I start the RI return, as you said, it shows $200,000 in the box for wages and salaries, but you can see that the instructions say to enter the portion of your o$100.000 in wages and salaries that you earned from Rhode Island sources. 

So while I see how this can be confusing, all you need to do is enter the correct portion of your RI  wages in that box.  Continue through the interview, apportioning the all other income based on the state where it is sourced. The $200,000 that carried over from your W-2 will not be  entered anywhere on your RI or MA returns. You will see the allocation of income on Form RI-1040 NR, Schedule II, Full Year Nonresident Tax Calculation.