Are you playing the single player storyline, or have you finished that? I ask because in the storyline, the game will lock jumpholes, change specific items faction reps (so you cannot dock with some items - like a tradelane, a jumpgate) and more. Essentially, during the storyline - once you leave one area - you aren´t allowed back until the end of the game. If its not during single player, I would urge trying to get a little more friendly with them first - it may just be a borderline rep issue. The other alternative is that one of their chums hates you (like Rogues or Outcasts) and that they have a ship in the area - at which point they will all attack you.
