But there is nothing in the story stating NYC is returning the effectively stolen, as per their admission to wrongdoing, money.

It's not stolen, that implies an intent to do wrong. Per the NYPD's response (and given their candor, I find no reason to believe otherwise) it's clear this was a training issue and the officers writing the tickets were doing their duty to the best of their knowledge at the time.

And having said that, yes I believe the money should be returned, and probably will.

They sent an email saying they made a mistake to a blogger.

Not by the officers.