My wife and I live in MA and have income in both MA & CT. TTax says do the CT return first. When our income is brought in we see 300k income vs. what should be 200k

If CT is your non resident state, then you will need to be sure that the non resident state return is what is being filed and then walk through the steps to the question regarding adjustment of income.  Here you will remove the income that was earned in MA and is not a CT source.