This is second hand from someone close, but not too close in the military, so details are off but the narrative is on track:
The Mercy was deployed after some communication between New York hospitals, and the understanding at least was that it would mostly be handling emergency, trauma, and routine patients (what military docs are good are at as a stereotype), and free up capacity for the hospitals to deal with COVID. The "normal" medical stuff promptly dropped in demand with lockdown, between fewer accidents and deferred care. So there wasn't much for the Mercy to do, the few covid patients sent over were about all of an "unknown air transmissible virus" (working theory at the time) that it was really equipped to handle, because that wasn't the mission they were expecting.
That makes sense in New York but we knew more about the situation when she was in LA and when the USNS Comfort was in New York later on. (Also I put USS Mercy when it should be USNS Mercy)
"Another of the Navy’s two hospital ships, the USNS Comfort, was sent to New York City to treat non-coronavirus patients. However, after treating only a few dozen patients, the Comfort changed its rules to allow coronavirus-positive patients on the ship.
The Comfort had been docked in New York Harbor in Manhattan since March 30 but departed last month for its Norfolk, Va., home port after treating just 182 patients."
https://news.usni.org/2020/05/15/usns-mercy-leaves-los-angel...