1) They take you out of the game since they're meant for the player, not the character. It's as if the GM said that, to beat the BBEG of the game, you had to beat him in Super Smash Bros. This breaks narrative flow and immersion.
2) They break roleplay. You are not your character, nor you are obligated to. You are not presented with vector calculus sheets whenever your character needs to land a plane. You are not required to narrate the full procedure when your character is performing surgery. You are not required to study at the police academy and then take the detective course to play a private eye. Whenever your character undertakes something you can't, that's where the skills, attributes, and dice come in the picture.
Warning: This only works in cartoons, or in campaigns with overbearing, micromanaging GMs
3) GMs are rarely (if ever) actual game designers themselves. I say this as a GM: "Clever puzzles" usually aren't. Descriptions always seem clearer in our heads than the way they're actually conveyed to players. The solutions to each puzzle are always "obvious" to us because we wrote them; as GMs, we play with a full deck. Truth is: Our descriptions are usually as incomplete as our clues, which means players have as easy a time trying to solve our puzzles as a female creator trying to get to the top in Marvel comics.
(Tip: Ask Chelsea Cain about her feminist agenda).
Puzzles are something I lump straight with bait&switch, BDSM, and playing Numenera. If the whole table is into it then go ahead, more power to you all, but never force it on the unwilling, and be aware that the lesser your degree of expertise, the higher the chances of one or more of your players flipping the table on you.