Sounds like the boat had waterjets.
In the "jetroom" or lazerette, there are access hatches on top of the jet tubes which are just above the waterline by inches. But only to be used if the jets are clutched out and not engaged. They are there for clearing debris that might get in the impeller.
If you take that hatch off underway, well you can imagine what might happen. Like...... the boat might sink.
I have seen this before, where somebody didn't put all the bolts back in the hatch tight enough. It is amazing how fast that jetroom fills up. I have also worked with former NYPA personal before. Doesn't suprise me.