So i was traveling from Winterhold to Windhelm, when i came across a bear. I decided to run. While running, i came across a bunch of imperials with a stormcloak prisoner. To my suprise not only did the imperials attack the bear that was following me, but so did the stormcloack prisoner...with HIS FISTS (which should have been bound...but they wern't). They gained up on the bear and killed it. Then in that same area i saw a Frost Troll which i attacked, it came at me, but since the imperials were still in my area, they and the prisoner attacked the frost troll as well and killed it.

As this ever happened to you? Have you ever seen Stormcloak and Imperial AI working together against a common enemy that would attack them both?

They doesn't seem to stop fighting over a fort when a dragon attacks.
They rather want to kill each other, leaving the dragon to me.

Well...not sure if that counts, had a bug once, that when I wanted to help my fellow Imperials against a group of Stormcloaks on the Road, I got a bounty and both groups ended up attacking me -.-

Well I think it is more of a survival script then working together. I often hit patrols escorting prisoners but I have never seen the prisoner help by attacking his captors but they will throw themselvess into a fray against NPC attackers.

I have seen Stormcloak and Imperial patrols working together to take dragons, but this was due to their AI regarding the dragon as the bigger threat than each other. As soon as the dragon moved away they started killing each other again.