Well, I lived the same thing.
I thought that was because I tried to go around too early in the game.
There is no way to stop this (even by suppress the pirate with the debug option, your ship will explode within take a single shoot - pirate are just there to give you a reason to lose)
So I restarted a game (gratefully you are not far in the story) and just followed the quest line (until you get the blue pirate ship). Ans then, I did not meet this issue again.
Have a nice day
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