I've seen the A.I attack islands many of times and then take there stack away when the mission is done and usually leaves 3 units behind.

Since you gave the city away that army no longer has a mission. The other problem is this army is probably not causing a transgression problem so they do'nt get an incentive to leave, funny how the A.I is immune to transgression I think. As if I had an army parked in neutral territory that long it'd get attacked.