My space map contains 3 star destroyers each with their own spawn paths, landing region, death region and vehicle spawn. But for some reason the AI (Imperials) are shooting their own star destroyers and it seems to always be in the same spot being above or below the hanger. Anyone have any ideas as to what the problem may be? Thanks

You need to make sure there are no items nearby that have the opposite Team value. When something is given a Team value (usually 1 or 2) then the opposite teams (1 or 2) will be set to attack it. Changing it to 0 (neutral teams) should fix it.

I found out that they are also shooting nothing, just firing shots into space. I checked the objects and everything is set to team value 0. Besides the star destroyers destroyable objects such as the sensor, life support , etc. Also the turrests are set to team 2 (Imperials).

EDIT
Also my map does not contain any rebel capital ships which for some reason made the space hud on the top right ingame have the star destroyer red with nothing to destroy and the rebel blue with things to destroy when playing as an imperial. Sorry if that doesnt make that much sense.

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I can't fix your first problem, but the issue with the backwards icons may be able to be fixed with this:

http://www.gametoast.com/viewtopic.php?f=27&t=6298