Yes I remember to have read that in the TWoS thread, some enemy ships could remain stucked in following you. It's proposed to save and reload game to fix.
I have yet to see this one, must be kind of nasty, try to reach a friendly port with your 'escort'..
Maybe it has to do with the use of TC. I remember in SH1 if you use TC > 16 then all enemy ships will magically come over you after you escape them... Maybe a heritage of this game.