One (most likely very old) bug I detected when playing at medium difficulty.
Battle 3 Mission 7 - Scramble!:
I disabled Shuttle AA-23 in Region 2 (after the first jump from the Liberty) and won the mission after Storm Unit brought the shuttle back to the Liberty. Then I destroyed ISD Imperator which caused the shuttle to be destroyed as well and the mission to be lost although the shuttle wasn't even in the same Region. Haven't found a solution for this problem with AlliED.