Continuity mistake: Carmen is wearing white sneakers riding with Juni on the magnetic transporter. After jumping off the magnetic rider and entering the hidden temple, Carmen is wearing black sneakers.
Continuity mistake: On the sub, Gregorio and Ingrid are talking to Ingrids parents about the fact they shouldn't be going with them to save Carmen and Juni, and her parents are putting metals flasks down on a side to the left of the grandmother. The flasks are always visible, then the grandparents both activate cool spy gear on themselves, and in this wideshot the flasks vanished. (00:59:20)
Revealing mistake: At the scene where all the spy kids are fighting the waiters, watch Gary as he is fighting. The waiter he is fighting throws him back, but then Gary activates his rockets shoes. Yet to activate those shoes you have to tap them together. The rocket shoes activate a few seconds before Gary tapped his heels together.
Continuity mistake: When Carmen and Juni realise they've gone around in a circle, they run through the room of treasure again. There are some gold pots near the sword which Juni grabs later. In one shot they run past the gold pots, and one pot rolls across the coins. When it cuts to Juni grabbing the sword, the pot is back to it's original place, and the pots and coins as well as the sword differ their position between these shots too. (01:10:15)
Revealing mistake: When Carmen and Juni are standing with a mountain as a backdrop, you can see Carmen's reflection behind her. (00:48:30)
Continuity mistake: Juni has his electronic bug tie his bow tie for his tuxedo; in the same sequence you can see a small part of the metal clip on Juni's clip-on bow tie.
Plot hole: There is supposed to be no power when the Dragonfly ship reaches the island, but the lights are still on. At first, I thought it was just a lighting trick, but you can see the lights are on in the tunnels.
Revealing mistake: When the kids are attacking the waiters, one of the waiters jumps intentionally onto one of the tables without someone pushing him.
Audio problem: When Juni falls into the "volcano", Carmen attaches a harness to a branch and dives after him. She grabs him and then seconds later the harness snaps. It then cuts to a shot of Juni and Carmen plummeting down the volcano, and you hear Carmen yell "Juni!" yet her mouth is shut tight. (00:48:05)
Continuity mistake: When Juni is eating spaghetti in the kitchen, his spoon is empty. After Carmen speaks to him, he has plenty of spaghetti on his spoon, without putting his spoon near the plate.
Continuity mistake: In the scene when Ingrid and Carmen stand by the vanity table putting on makeup, talking, in a wideshot Carmen puts a tube of lipstick onto the table and puts her empty hands on her hips. Then when it cuts to a closeup, she has both hands up near her face and a tube of lipstick in one hand too. (00:07:50)
Continuity mistake: On the sub, as Ingrid and Gregorio are off to save Carmen and Juni, Gregorio hears a noise and goes to open a circular metal door. It turns out to be Ingrids mother. Gregorio then opens the circular glass window, and she climbs through. As she climbs through, Gregorio's left hand leans against the wall, and he lowers his arm to his side. It cuts and his hand is then instantly back against the wall, and he once again lowers his arm. (00:58:30)
Revealing mistake: As Juni runs to save his sister from the skeletons, he fights two of them (one wearing a helmet) before running out to the rocks that she is standing on. After he defeats the skeletons and runs off screen and immediately before the scene is cut to show the outcropping with the kids on it, there is one frame where the skeleton disappears from the shot immediately before the cut. (01:13:55)
Continuity mistake: When the father is playing with the yellow thing in the office, the mom comes in and he puts the toy on his lap. Immediately after, he still has the toy in his hand and then puts it down, again.
Continuity mistake: After Gerti and Gary fall in the camel poop, their clothes are clean, even though they are the same clothes they had on when they fell in it.
Continuity mistake: On the floor, behind where the skeletons stand is some assorted treasures, like vases, boxes, pots, scrolls, coins etc. The treasure on the floor [near the gold circle on the floor, which is clearly visible when Juni snatches the medallion and legs it] changes [eg. thing appear, disappear and change position] from when Juni ponders about taking the medallion, to when he takes it and runs. (01:09:00 - 01:09:45)
Factual error: Juni is sending the bad twins to Gobi desert. After few scenes, we can see the bad twins in the middle of Gobi desert. They get there with a submarine. How can they enter to a middle of the desert with a submarine inside the water?
Continuity mistake: When the spy kids first meet Romero, just before he says "It's science," we can see him push the lever to turn the small island's volcano, but in the next shot or so, we can see that it is off. (00:49:50)
Continuity mistake: As Gary and Gerti make it to the beach, Gary says he is going to "zap" the monster in the ocean. When they show him trying to zap the monster, his watch strap is undone, but when it cuts the strap is now secure.