Also part of the problem is you have to realize that the MA server isn't all that responsive (or maybe it's just the load it's under). Make your edits and WAIT a few (maybe even five) minutes. It doesn't update immediately sometimes. It takes a bit. I ran into some hassles with that myself yesterday, but it all worked out when I slowed down.
Dec out.
Let me get this straight.
Mission Enemy Faction = Main
Boss Faction = G1
Boss allies Faction = Group1
The mission would then spawn enemies in "Main" as normal, but their faction would display "Group1" or "G1" depending on their rank?
If that's so, that's some bug you got there.
I had a simular issue. I have random civilians to be saved from the pre-made group. If I make it a mission objective, they show up as normal, but if I made it optional, the citizens would use random models of the mission enemy excluding EB/AVs.
Freeedom
H: Victra Defile (Rad/Dark) & Hot Hits (Fire/SD)
V: Spike Cream (NW) & Crescent Wind (Nin/Storm)
Sub Hero Inc ARC: 1541
--If you don't like what I have to say, it was probably a typo you are refering to.
Sounds like you ran into the custom critter naming bug. Very annoying, but at this point there's sadly nothing you can do about it. Just set the names correctly in your editor window, make sure they're correct in the .storyarc text file, and hope for a fix to come someday. 
"If I had Force powers, vacuum or not my cape/clothes/hair would always be blowing in the Dramatic Wind." - Tenzhi
Characters
Decorum - yes I should have taken a break but I didn't want to leave a mess to come back to. When I got it fixed I saved a backup and moved it to a separate folder. (I'm not paranoid. Nope 
)
Optanite - Yeah, it was weird. It may have been due to editing too quickly. It was fine later.
DeviousMe - I think that's what I clued in on. I had read about the bug with "all custom enemies" but never dealt with it. I eventually went from the character file for the boss, and the two group files, to the actual mission/storyarc file and made the changes. (I did this all from the MA of course).
Yeah. My problem was editing my existing arc. I had a lot of cut and pasting and my comp is weak and doesn't work well with other windows open. So I was "republishing" after every paste, and then going back into the edit. I didn't notice until later that it wasn't updating quickly enough, and I was ending up pasting something and saving, where the previous paste hadn't taken yet, so I was saving what I'd edited away previously. I spent about an hour doing that before I noticed it. **cries**
Dec out.
Cut and paste is something they need to improve. I got a "invalid blank space before x" type of message. That's what lead me to editing in Wordpad and losing the whole test file.
Now I just type and patiently putter as I don't trust cutting/pasting in MA yet.
Being able to check the html would be nice too. We don't need to see MA specific code - just the parts that effect how text appears in a mission.
Fun and Frustration 2
The fun continues. As I said before: adding second mission messed with my groups in Mission 1. I fixed Mission 2 checked it over and it seemed okay. Mission 1 still had the name issue. I change the boss setting to "single" for the enemies so he is alone. Voila, both missions seem okay. Save/backup files and exit for the night.
Character: wp/fire tank level 50 on tenacious.
Last night/this morning: I tested with my level 31 Plant/Storm controller on heroic.
The good news is that the main custom group was manageable. (They can be tough for melee types on tenacious). Also the group names in mission 1 were right.
Mission 2 was ... interesting. The minor groups/bosses took on the faction name of the main group if the map spawned them close to each other.
-----------
Mission 1
Two groups
Group1 main enemy group used in all missions. Minions, Lts, Bosses.
Group2 Lt is ally. After I added the same boss to the second mission as an enemy this boss took on Group1 as his group name. Setting him to "single" ie: no guards fixed the name problem.
Mission 1 seems fine now.
----------
Mission 2
Group1 is the same minus any bosses.
Group2 the ally from the previous mission is now an enemy. His guards are Group2a and guard an object also.
Group3 consists of one boss.
Problems:
Sometimes Lts from Group1 take on the other group names.
Consistantly mobs in groups 2, 2a, and 3 will take on the Group1 name if the map spawns the groups close to each other. The map is an outdoor unique.
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The objectives and sequences seem fine. It's just the name bug that is annoying.
One things I can try is using another non-unique outdoor map.
Hmmm...maybe it's something as simple as you needing to name them less similarly?
Or are these merely example names?
Dec out.
Examples. The main group could just as easy be "Bugs"; the ally/enemy: "exterminators boss" for his group; his minions: "exterminators"; the other boss: "others" group. So basically:
Bugs - main group mostly with themselves.
Exterminator boss appears with Exterminator guards. (another group guards an object).
Other boss has to have minions so he's paired with the bugs - although it doesn't quite fit.
If I could make the two bosses be beside themselves it might fix the problem. I tried making them rogue but that didn't work.
I'll also try another map (sigh) and see if that works. I added a bug report to the i14 bug thread too.
I wish there was a way to lock certain parts of a mission or other parts of an arc. I'm working on a new arc with two missions - so far. Things are coming together but I found a MA glitch that made over an hours work for me.
I had just edited some text and rechecked one boss and his cronies. I had to give the boss his own group (call it G1) or he would spawn multiple times in the missions. Call his men "Group1" and the main group "Main".
First of all the main group took on the other group's names. The minions Group1 and the Lts G1. I rechecked and resaved. The main group had the correct name but the other two were also "Main". Recheck and save. Group1 is then fine but G1 is still Main. I fix that and then the problem reverses.
I think part of the problem is "Group1". They guard an object by themselves but also spawn to guard the boss. Either the MA saw the two spawns as seperate or else I kept over correcting one or both.
What a pain anyway.