I'm not sure if it's a bug or working as intended but in skirmish mode clone trooper spawn in as a platoon of individuals, where as in GC they spawn in squads of nine. However when they spawn especially on defensive battles they are spread out and then come together to form the squad. The clones themselves also do not have the ability to Take cover, even though its listed. As stated earlier, I'm not sure if it the intention or a bug as I haven't been able to find anyone else with this issue.