You might be getting this notice if you did not choose the correct Box 14 category while inputting your W-2. If your 414(h) contributions were made with pre-tax dollars, you should have chose "NY IRC 414(h) subject to NY Tax". If your 414(h) contributions were made with after tax dollars, you should have chose "NY IRC 414(h) NY tax exempt". Your choice will determine whether there is an entry on Line 21 on your IT-201, under Additions to NYS Income. Please see screenshot below for an example of the W-2 input screen.
From your question, it seems as you are stating that the 414(h) contribution was not on Line 21 of your IT-201. Can you clarify what category you chose while inputting your W-2?