What’s complicated is that despite the idiocy of having the U.S. military pick up a group of mutants at sea who were firing at a Navy vessel instead of dealing with them on the spot ... these mutants ended up in a U.S. court that had to deal with a bizarre legal question that I don’t think any objective judge could really address.
A ship on the high seas retains the nationality of the flag it flies. Otherwise, you'd be saying that no crime committed on the high seas could be prosecuted. The pirates were properly brought to the United States for prosecution is a civilian court.