It may have something to do with the map. Are you using the villain tutorial bunker? I know that only has a couple spawn points, which would be taken up by your ally and boss.
No, it's the cargo ships (cargo 4) and both the boss and ally are supposed to spawn with enemies around them. Neither of which show up (the enemies, the boss and ally do). So basically, you got a 'captured' hero with no one guarding them, and a boss who talks to himself 
What villain group are you using? I'm having the same difficulty with the first mission in one of my arcs using the Family (5-40). In this case, none of the mobs are spawning, even the boss mobs that I placed. I switched the enemy group to the Freak Show, Longbow and they worked fine on the map. Switch back to the Family and no enemies spawned again.
Yep, Family (5-40).
Least the problem has been duplicated now.
It is a know problem with the Family in a certain level range. They are in the game at that level, but only on the Rogue Isles. A switch is set somewhere in them, so that those levels of Family will only spawn for Villains in MA. There are one or two other groups have that that problem, one of them only spawning for Heroes, but I can't remember which they are at the moment.
Justice Blues, Tech/Tank, Inv/SS
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Fighting The Future Trilogy
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Carnies don't spawn properly for heroes below 40. Snakes are also wonky.
I think the level 30-40 Family issue going on now is different, in that they are not spawning at all, for anyone, whereas before i15 they would spawn at 40 for heroes and the correct level for villains. At least, that's my understanding of what's happening, as I don't have any arcs that contain Family.
Eva Destruction AR/Fire/Munitions Blaster
Darkfire Avenger DM/SD/Body Scrapper
Arc ID#161629 Freaks, Geeks, and Men in Black
Arc ID#431270 Until the End of the World
So, I'm new to Mission Architect, and I looked a bit but didn't see the answer to this question.
I'm trying to make a story arc (big surprise), and I have all the text and options done for the first mission. Only, when I go to test it, no enemies spawn inside it. The boss for the end mission spawns, the ally spawns. but no enemies spawn.
Is this just something for test mode? Or did I miss some obvious button somewhere? I selected the enemies for the map, have checked that a few times.
Any other ideas what it could be?