The weakness/vulnerabilities in the villain's monsters are the result of:
DEVELOPER OVERSIGHT
Your villain is evil, yes. Has grand plans to conquer the world (know to strategize in general), yes. But not overly specialized nor qualified to build their entire army of minions alone, by their own hands. They employ several minions, either by contract or by force, to do the legwork of designing, testing, and building the monsters. Your villain is simply supervising the entire process after laying out their expectations on what kind of monster to build.
I'm going to quote Doctor Strange (2016) here to establish my points:
The Ancient One : The language of the mystic arts is as old as civilization. The sorcerers of antiquity called the use of this language "spells." But if that word offends your modern sensibilities, you can call it a "program". The source code that shapes reality.
Your villain's monsters are built using/upon these spells. These ancient source codes. The villain's minions simply utilize these spells as tools/materials to build the perfect monster ever as required by their employer. (Analogous to a team of software engineers creating an application).
Given these codes' antiquity, lack of proper documentation, incomplete examples on edge cases and corner cases of the spell's uses, etc., the villain's minions CAN stumble upon some undocumented behaviors of certain magic's invocations. Sure, they test the product before finally delivering it to the boss, but there are many reasons why such bugs can escape the testing process..
1. "It's already nearing deadline. 227
We have to finish the build by tomorrow." and thus they try to wrap things up in a hurry.
2. "The boss won't know anyway. We've been paid. We're done." said the minions. "Once he finds these weaknesses, it's too late already for him to track us down."
3. "These large weaknesses do not show in our laboratory-conditioned testing chambers.."
4. "Eheheh, I have made sure that these weaknesses only show up when the monsters are deployed onto battlefield!"
5. "Meh, I don't know it can do that. I can fix it just before next battle. Maybe. And that's if boss survived. The protagonist looks like he can defeat him fairly easily." 627