Some enemy groups just hate each other. What are the enemy groups in question and what detail are they part of?
What shall claim a Sky Kings' Ransom?
PPD & Resistance Epic Archetypes
By default they should never fight each other unless one is set to enemy and the other set to ally, or one/both are set to rogue.
I have seen some weird behavior in regular missions lately though. Last night in Scirocco's 1st arc we found Serafina's allies attacking her when we got to her room. No one in there was marked ally to us, they were simply hostile to everything which is not how that mission worked prior to issue 15.
At first I tried putting ghosts and werewolves but they were fighting eachother. So I made them all werewolves and decreased the number in the battle but they still fight each other.
If you are using the Battle objective, they are set to hostile to each other, no matter what the groups are. Whether or not they are hostile to the PCs is set separately, but there is no way to keep them from killing each other. This is actually a very nice feature, I have one mission where as soon as you enter the warehouse, there is a huge melee going on in an apparent civil war in the group. Blasts flying everywhere, swords swinging, it is really great. If only they get the bug in the final map of the arc fixed, so I can publish the sucker. 
Justice Blues, Tech/Tank, Inv/SS
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Fighting The Future Trilogy
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I'm having similar problems like this in a mission I just made. Enemies that shouldn't be fighting each other are. Example: A patrol of hellions that is supposed to be working alongside my custom group is attacking the custom group if they wander into them.
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If you are using the Battle objective, they are set to hostile to each other, no matter what the groups are. Whether or not they are hostile to the PCs is set separately, but there is no way to keep them from killing each other. This is actually a very nice feature, I have one mission where as soon as you enter the warehouse, there is a huge melee going on in an apparent civil war in the group. Blasts flying everywhere, swords swinging, it is really great. If only they get the bug in the final map of the arc fixed, so I can publish the sucker.
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The only other annoying 'bug' (athopugh I don't think the DDevs considered it one, it's just an artifact of 'Battles') is if you also have any Patrols that are the same group as one of the groups in your Battle; the Patrol will attack the remaining MOBs of any Battle group they come across EVEN IF the survivors are the same group as the Patrol. I've tried numerous things to minimize this in my MA arc, but it's just a known behavior of the MA MOB AI system.
I'm new to the Architect creation. I can't seem to get the enemies I've placed to not fight each other, even tho I switched them all to the same type.