Plot hole: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.
Plot hole: Cruise leaves Lugnut to go buy he and Coupe some seats and mere seconds after leaving, Coupe appears in the scene and talks with Lugnut. Coupe asks if he has seen Cruise, but even if Cruise had already left to go buy tickets, Coupe would have already seen him when approaching Lugnut since she only arrived seconds after he left. (00:09:15)
Plot hole: Alberto didn't sign up for the Portorosso Cup, and he enters anyway. This should've gotten Luca disqualified.
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.
Plot hole: During the final scare event, Mike gets a perfect score because Sully broke the simulator to allow the 6th scarer to get a perfect score no matter what. After the contest, the simulation resets and Mike pretends to scare the child in the simulator and it registers a perfect score on the scoreboard for the 6th scarer when it should really have registered a score for the 1st scarer, because the simulator had been reset.
Plot hole: Rafe is not a supernatural being, and besides not suffering any fatigue at all missing his sleep to do his pranks, some are outright impossible to execute and perform overnight for a person of his age (most likely for an adult in their prime too). Covering the entire hall and corridors, plus the principal's office, with post-it stickers requires a ridiculous amount of stickers to begin with, and arranging them creatively covering the whole walls, floor to ceiling, so that they create drawings, is an insane concept. Even more insane when it's the opening prank, anything he does later in the movie including the big movie finale requires less labor and time than his first act did.
Plot hole: When The Ray is injured on Earth X and has Red Tornado's cortex, he escapes by Vibe sending him into a portal to safety. However it is evident that Vibe doesn't know where he sent The Ray or where he would be going as later he's trying hard, searching the multiverse for him. Yet somehow The Ray is able to go across universes and winds up coming out right at Earth 1's Ray's feet to transfer his powers over to Ray and give him the Cortex. This makes no sense. The Ray can't control Vibe's powers or where he sends him, so he would have had no way of making himself exit the portal in Ray's back yard. And if Vibe sent him there on purpose, he wouldn't have been struggling to figure out where he went. The only way it makes sense at all is for it to be the most massive co-incidence possibly imaginable where he accidentally was sent to another universe and happen to come out right at the feet of that universe' version of himself. None of it adds up. (00:09:50 - 00:16:50)