Don't hide the weak point
Think about video games that implement puzzle bosses or bosses with a single critical weak point. Often, the hardest part isn't finding the weak point, it's figuring out how to access it. House of the Dead straight up shows you a diagram of the boss's weak points before every boss fight, and Shadow of the Colossus is basically just a series of puzzle bosses with glowing blue weak spots all over their bodies. Actually hitting those weak spots, though, is generally a test of skill, accuracy and reflexes.
I recommend revealing the weak point as soon as the battle starts, in the form of an aspect. Explain that the weak spot is well guarded, and will require some fancy fighting to access. Give every player a free invoke on the aspect, to be used only if they've figured out a way to access the weak point. Alternatively, you can continue to allow knowledge rolls to find a weak point, and then give a free invoke to the player who discovers it.
Hidden weak points make good challenges in video games because once you've discovered them, you still need to be quick and accurate enough to hit them. In tabletop roleplaying games, physical accuracy and reflexes aren't really a factor. So if you want to translate puzzle bosses into Fate, you're going to need to translate the challenge into something that Fate handles well...
Instead of reflexes, reward creativity
There are two ways you can go about this, depending on the level of agency you want to give your players. The first way is to pre-design a handful of environmental aspects that can be tagged to help expose a monster's weak point. You can use these aspects to create a traditional puzzle boss feel: you need to shoot the rope to drop the boulder to crack the shell to stab the baddie's organs. This can be fun if you make the puzzle rewarding enough to figure out, but Fate probably isn't the best system for that kind of play, and your players may end up feeling railroaded within the combat.
The other option, the one more in line with the spirit of Fate, is to provide some useful environmental aspects, but encourage your players to create new ones with the Create Advantage action. With this approach, every move becomes a brief and focused action sequence where players are challenged to narrate how they could possibly strike the monster's weak point. They'll spend turns setting up traps and giving each other free invokes, then spend them all on one epic strike at the monster's vitals.
This is how Fate combat is supposed to work anyway
Combat in Fate is about modeling the decisive moments in a battle - just the really really cool attacks. Fate is a storytelling game, first and foremost, so any challenges you build should be geared around telling a good story.
Basically, give the players the tools to start telling a good story about the combat, and reward them for doing it.