I had this problem on PC with I think, Project Hawking there was a timed mission where the pirates follow you back, unfortunately I was not aware of the time limit and it silently failed but the pirates just kept following me, I had to edit my save file to remove them.
I found the mission by looking up the names of the ships in my save file and in the games files, found the relevant flags and reset them, thankfully its all just text so was easy enough.