To make it look less arbitrary, write it into the quest ahead of time. Let the Hero's have their "winning strategy" (and even let them breeze through a quest with it, sounds like you already have) but plan ahead to work around it for next time. Kudos to them for finding a brilliant cooperative tactic, but you're trying to prevent it from getting boring through lack of difficulty.
A double wide door sounds cool but four heroes could still cover it if they are determined, and back to the same "problem" though it would force them to stick together.
Several ideas come to mind...
When you see these bottlenecks in your quest map, equip some of your monsters with staves or spears (why not?). You could have a Gargoyle that can use his whip as an alternate weapon, etc.
Add in monsters with ranged weaponry. Sure they can't shoot through each other, but even official quests will have traps in the room that monsters are hiding behind (to lure the heroes in, after all, monsters don't spring traps).
Put a spear trap right in front of the door, that can freeze the first hero in place allowing him to get hit (and feels less unfair than putting a pit trap although that can work too).
Undetectable secret doors can be added that the monsters can trigger in circumstances you lay out in advance, allowing monsters to pour through and flank the heroes. You can even add a completely undetectable room nearby for this purpose where reinforcements will come to bail out the "besieged" monsters. This isn't cheating.
Also, consider monster placement. You can put the monsters starting out right in front of the door, and on the sides, or several squares in. Maybe design it so that the Heroes are supposed to enter the room to progress to the next point and the monsters are behind furniture or something.
Imagine a doorway, with a hero on one side and a monster on the other. What happens? The hero will attack and his buddies will throw diagonal attacks on the monster. But if the monster doesn't die instantly, guess what happens on Zargon's turn? He gets to attack, then move out of the way and another monster can move up and attack, repeat. If it's an Orc, oh well, but if it's a Mummy or Fimir? They might be in for a time there. I've killed Heroes using this technique.
And what about magic? I say this is a sticky area where it could start to seem abusive so be careful, but there are even official quests where some monsters have magic. It doesn't just have to be the big boss at the end. Maybe give a Fimir a Rust spell or a Tempest. Maybe some Mummy has a Fear or Sleep spell. Zombies are nothing right but what if the Zombie could "infect" others... give him a "Command"! That might break the game, but I just thought of it now, give it a try once and see how it goes.
The goal isn't to make it so unfair that they always lose, but I agree with you if it feels to easy and they abuse this technique, then shaking them out of that complacency with good pre-planning is a fine idea. And sometimes Heroes get great rolls and Zargon gets crappy ones, those are the breaks!
There's also Evil Wizard cards and Chaos Combat cards, to give the bad guys another chance if they go down too easily (they're random draws so it's fair). Maybe the card lets the Hero's attack miss, or lets a particular monster use blue dice (count white shields essentially) for defense, or he can regain a lost body point, it doesn't have to just be for named "boss" characters... pick a Chaos Warrior, Fimir or Mummy to be the one.
In fact, swapping out a basic monster for a stronger one or two can really make a difference in the above. Instead of two skeletons, make it two mummies. Instead of two Orcs, make it two fimirs. Got some Chaos warriors? Make one of them a Gargoyle (Gargoyles are notorious for seeming to be paralyzed stone statues who suddenly come to life when you least expect it)! All of a sudden, its not such an easy thing to clear the room this way.
There's one card in the EWP about a mimic monster. Why stop with one? Maybe there's some seemingly "empty" room where the furniture comes to life. Suddenly those tables and bookcases, etc. are roaming around throwing attacks. It doesn't have to kill them, but just keep them on edge with the unexpected. Just remember more monsters means a longer quest. You can try to force them to run, but it's hard, a lot of players will just stand and fight thinking they can overcome the odds. Sound the "alarm." Rally the troops, suddenly the monsters get to be elites and roll black dice to attack and blue dice to defend (this is a very dangerous proposition, even mere Orcs will become very threatening to most heroes). If they are dropping like flies, maybe give them an escape route, put a delay between waves of reinforcements. Give them a chance (even if a slim one).
At some point I plan to add battle tactics to the game... formations (find the scrolls of battle that allow you to learn these techniques). So Heroes clustered together get bonuses (using green dice to defend for example in a shield wall, or black dice to attack against a single foe or as they all shoot ranged together). But I'll be giving the monsters similar options too! And then there are those lone monsters you could "parley" with to try to eliminate or squeeze a little bonus treasure out of (or maybe they suddenly get a perk like calling in another monster or getting a cheap hit on you).
But whatever you do, if possible, I'd say don't always use the same strategy every time. To keep 'em guessing, but don't overdo it either, like you are breaking the entire game just to stop them ever employing that strategy again. The simple placement of some slightly stronger monsters can make a big difference and if you have to install a few undetectable secret doors with optional reinforcements, so be it.
Being Zargon is fun, toying with the heroes, but you probably like many don't want to beat them so hard they give up playing with you altogether, if they think they can't trust you anymore.
We are still talking Game System/KK/ROTWL here. When it gets to crazy quests in EQP/BQP and Dark Company, I think allowing the heroes to "cheap" or "cheese"

certain monsters probably won't seem so bad, because it may be the only way they can survive certain situations!
Make the brash, cocky Heroes feel a little less secure... not so they think you're a vindictive cheater, but just let them fear a little. If they pass your little tests, reward them. Toss in a little extra treasure, maybe a cool potion or scroll or something, maybe a neat side mission for their bravery. Maybe they can save a prisoner who will fight for them. Who knows! Playing Zargon is fun, this is a great opportunity, and I'm excited thinking about it myself, have fun!
