I know, right? You slave for years on your pet project, eliminating every single flaw, refining and improving your product for maximum effect, then release it into the world to impose your will... and some peon finds that flaw you never noticed, and suddenly your whole plan for dominance falls apart. Worse, you pore through the plans for hours, recreate the flawed parts from scratch, and it still won't go away.
And that's just the programmer's perspective.
Your antagonist probably isn't dealing with Heisenbugs. I think it's more likely that he's facing one of a few issues:
He very literally cannot see the problem. For some reason that glowing "kick me" sign just doesn't register in his sensorium. When he reviews his creatures all he sees is a patch of hide, maybe a bit weaker because of the way the creatures' armor fits together, but nothing out of the ordinary.
Perhaps it's analogous to color blindness - maybe more than just analogous. His big green killing machine just happens to have a bunch of red arrows pointing to the weakest point, but he can't tell because they look the same to him. Less directly, the leakage from the creature's core/power source/whatever is on a frequency band his species just doesn't have the ability to perceive, but which is super obvious to other species.
The conditions in the lab/foundry where he's creating his monsters are such that the weak points don't actually manifest. The weakness is still there, just not on the surface where it's obvious. Once the creatures go out into the world they encounter conditions that bring the weak point to the surface. He'd actually have to be following the creatures around through different environments to observe the effect.
Nothing is actually wrong with your creatures, somebody is screwing with you.
Your perfect creatures are being changed without your knowledge once they're sent out. Some active magical effect is forcibly altering the creatures when you send them out. It's an insidious effect that you don't even notice until after it has happened, and whenever you try to defend against it the effect changes to bypass your countermeasures... if you're even aware of it in the first place.
You're working with spells and rituals you uncovered from long-dead civilizations, modified to your specifications, but the magic simply doesn't work the way you think it does. What you don't know - because the snippets of information you've unearthed simply don't mention it - is that the original magic was for creating arena monsters that are designed around the idea that the products would have a target zone to give the competitors a chance. After all, as fun as it is to watch your gladiators spill a little blood, it's really hard to get people to sign up to fight an actually unstoppable behemoth.
Maybe it's not actively working specifically against you, perhaps it's a global phenomenon. Anybody who creates monsters like you do will have the same problem.
Perhaps this is a law of nature created and maintained by the gods after a particularly nasty previous situation that required their direct intervention to prevent the death of all peoples of the world. I can imagine the gods getting together and blaming each other for it, arguing for a bit (possibly loudly) and then one of them proposing they just change the rules to make a repeat impossible.
Or perhaps it's a back door somebody left in the magic system when it was set up in the first place.
What, you think magic just happened? Have you seen how complex that stuff is? How many bits were clearly just bolted on to fix problems? Pull the other one bruv, I've seen enough badly-patched legacy systems to know one when I see one.
I know, he talks a good game, but he keeps pumping out these things that couldn't possibly complete the stated goal of taking over the world. But are these the actions of a true Evil Overlord? Even one that hasn't read the list?
Actually he's a guy who's just trying to make sure that people don't stagnate, or that the world has something to focus on other than petty tribal squabbles. He's seen what happens when there are no common threats to bring the nations together, and maybe he thinks that providing a focus for their aggression is going to be a major improvement over the constant wars over petty things.
On the other hand, perhaps he's trying to prepare the world for a worse evil that he knows is coming. When the stars align just right and a portal to a hellish realm opens, flooding the world with actual demons (who just happen to look a lot like his creatures), it would be much better if people have plenty of experience in how to deal with them.
Either way, he's just trying to save the world by killing half... I mean teaching people how to get along against a major threat.
And he's starting them off on easy mode. The monsters are big and scary, yes, but for now they're fairly easy to take down. When people are used to the idea he'll make them a incrementally tougher. In the "save the world from a future disaster" scenario he'll keep going until the people of the world have adapted to fighting the full strength monsters, hopefully before the real ones get here.
I started with two ideas, but that got a little out of hand. Again. Hope something in the list works for you.