Yes, I've heard of this happening before when they are "in pursuit" of a ship. If you are sitting inside their system and they send ships to sit next to yours preparing to attack and then you warp out they will try to follow sometimes. Then, once they've been exposed to "the outside world" it seems to change the neutral AI somehow and they keep trying to leave.
I'll tell you a funny story, though. I once decided that it would be good to put two 'neutral' empires in contact with each other so they could trade and generate more income for ME.
I 'gifted' a communications channel to each of them. They almost immediately declared WAR on each other and both started demanding that I break my treaty with the other! Even funnier, they started trying to send SHIPS to each others systems to attack! Yep, they were leaving their systems... D'ooh! Talk about a face-palming incident. I've never given neutrals any comm channels to each other since. I guess neutral races just naturally hate each other.