The penalty is not for paying the estimated taxes based on your 2017 income (which you had none). The penalty is for underpaying the 2018 taxes. Basically, you incurred the tax during July of 2018 but did not pay the tax until 2019.
Underpayment penalties are assessed if you don't withhold or pay enough tax on income received during each quarter. In fact, it's entirely possible to get hit with an underpayment penalty even though you paid your tax bill in full by the April deadline. It is all about the timing - specifically when the tax was incurred as opposed to when it was paid.
You probably do owe a penalty, but you should definitely make sure the NYS is calculating the penalty correctly as they tend to maximize the penalty in their favor, not yours.
You have the right to challenge—or protest—any Tax Department bill or notice that you disagree with. You can protest in different ways, depending on the kind of notice you received, and whether the time limit stated on the notice has expired.
Respond to your notice or bill online - You may be able to request a penalty abatement in your situation.
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