It sounds like you are working the credit for taxes paid to another state in the MA interview. MA taxes wages, salaries, pensions, business income, long term capital gains at 5% and short term capital gains at 12%. The total CT 5% income will be the total CT income from the 5% sources (according to MA); in your case that will be the W2 wages CT box 16.
You will also use the tax liability to CT on that 5% income source. The TurboTax warning is stating your CT tax liability is not necessarily the withholding listed on your W2 but the actual tax liability from your CT nonresident tax form. This should be line 16 on your CT NR form 1040.
In TurboTax online products you can "View the CT tax summary" using the steps below. You will find the income and the tax liability numbers there.
1. Select "Tax Tools" in the left hand menu
2. Select "Tools"
3. Select "View Tax Summary"
4. Select "Preview My 1040" in the left hand menu
5. Select "CT Tax Summary"
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