The add back goes on your New York return because the original deduction was related to New York source income.
When you have excess contributions, then if the contributions were made through the employer, the excess is added back to Other Income and you do have to pay tax on it. First, since it was related to New York source income, it's income for New York. I haven't tested it, but I am assuming that Other Income on the federal return will pass though to New York, so you probably won't have to do a thing...but I would have take a look to be sure.
The Other Income may appear on your CT return but I assume you will get a tax credit for the tax paid in NY on the same income, So you shouldn't need to adjust your CT return either, but do look.
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