While almost every aspect of NPC ships behaviour is at least weird there are some that may break game for someone. For me currently the most game-breaking bug in AI is "Escort Me" pathfinding and ships' behaviour after hyperjump. Let's start with the pathfinding.
Let's build two ships dangerously close (like really, really close) to each other and third ship somewhere else. Then give those two order to escort the third hit. It will take them several minutes and a high number of collisions before they will be able to start moving towards their escort target. That's not all. Sometimes when they reach their target, they will again move dangerously close to each other which will result in another silly situation.
Another problem is with hyperjumps. I have noticed that when you give your ship order to escort you, then it will jump with you. Then I have tried to do so with 8+ ships at once. Result was horrible. For some reason the ships after jump started spinning so fast, and they were placed so close to each other, that after one small hit they were destroyed and, almost, everywher (junk created after their destruction, to be more precise).
In general I think that collision avoid algorithm for AI could use some work and, when ships are part of a bigger group they should have some different behaviours (formation? distance-keeping? anything that could make them fly safely).