It is normal to see all of your income on the New York state return, even when you only lived and/or worked in New York for part of the year. New York includes all of your income in its initial calculations and then pro-rates the tax due (rather than pro-rating the income.)
You are correct that you should have filed as a part-year resident in New York but a full-year resident in New Jersey.
You didn't mention where you actually work (New York or New Jersey) as that can influence which state taxes which income as well.
It sounds like the total wages are correct at $55k, but it's not clear where you are seeing the number to be sure. It also isn't clear what you think is incorrect after the first amendment but if you can provide a little additional information to clarify, we can probably assist better.
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