These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Spy Kids
Big Lipped Alligator Moment: The appearance of the "real Guy" (played by Elijah Wood) in the third movie. To clarify, he just suddenly shows up, gives an inspirational speech... then he gets severely curb-stomped, booting him out of the game. He is never talked about again.
Fridge Horror: So if Minion was going to replace all the world officials' kids with robots, what was he going to do with the originals?
Fridge Logic: The children of the most important people in the world are all apparently the exact same age...
Ham and Cheese: Sylvester Stallone as The Toymaker in the third movie. He is clearly having the time of his life as a madman evil video game programmer who talks to holograms of himself as a hippie, a general and a mad scientist. Him sporadically shouting his dialogue helps.
Special Effects Failure: The 3D in the third movie is very poorly done, barely resembling 3D at all. Understandable, seeing as this movie came out when the advent of 3D was still trying to get on its feet, and the movie itself was filmed using a primitive version of James Cameron's 3D camera system.
The greenscreening is also incredibly blatant, especially during the fight scene at the end of the movie.
One from early in the first movie involves Ingrid moving her chair over to Gregorio. The track on which her chair is on is very clearly visible. Whether this is justifiable as yet another spy gadget's visible elements is debatable.
Squick: At one point in the second movie, Gerti and Gary wind up in a desert (due to Carmen and Juni's medaling) and are unsure of where they are. They fall into what at first seems to be a mud pit, only to look around and see camels surrounding them. Horrified, Gerti exclaims that it is, indeed, camel poop. Skip a few seconds into the future, and you see Gary opening his mouth and spitting a big chunk of...er, "mud" out of his teeth.
Toy Ship: Juni and Alexandra in the second film, and Juni and Demetra in the third film (with a Ship Tease of Juni and Gertie at the end, too). Carmen, who at least looked old enough to be interested in the opposite sex, only got an unreciprocated crush on Gary in the second film.