You are not the only one
I have launched my ship to empty seas as well.
Also ghost ships with the name above nothing and just a water swirl. But they can still attack and sink you, but you cannot sink them
Boarding ships especially collossus have been an issue with enemies that do not die even at zero health. One way my guild has found to save the cargo and get rid of that glitch is to have one crew mate get knocked out. The enemy then resets or something and can be defeated. Pirate sacrafice.
