I see a problem if Trump uses the military to handle problems that should be delt with on a state or local level without a request for federal help, or if they are us excessive force to squash demonstrations, protests, or rebellions by his political opponents or critics, like he has intimated. At least what I can think of off hand, but there may be more. Those are probably a little higher profile than an city's subway system. To be fair I could see Biden using the military if there is another election big lie and the extreme right people tries to storm federal government buildings again. I suspect it's a power that could be used or abused.
I don't quite understand how the NY subway relates to presidential use of the Insurrection Act if that is a point?.