Minor Plot hole: The remnants of a plane crashes in the ocean over Elastigirl and her children even though she transformed herself as a parachute to slow-down her family’s fall into the water. Did the plane slowdown in order to accommodate Elastigirl and create drama in the scene? Because as far as we know, a crashing plane has less air resistance than a fucking parachute.
Minor Plot hole: When Elastigirl leaves Dash and Violet in a cave in order to save their dad, she gives each of them a mask that was originally in her backpack. The problem is that when their plane crashed, they were left alone in the ocean with nothing but their skin-tight pocketless superhero outfits. So where did the superhero mother hide those masks? That’s a good way to start traumatizing children – especially considering that the kids then put those masks straight on their faces and never take them off until the end of the movie. Gross.
Major Plot hole: Syndrome, with the help of his henchmen and video cameras all over the island would know about all the powers of the Incredibles. It makes no sense for him to put Violet in the same electrical prison as the others (knowing that she could somehow interfere with the system with her purple electric shield ability) and even less to LEAVE THEM alone without any guards with machine guns to look after them. It's Austin Powers all over again!
Plot contrivance: When Mr. Incredible fights the Omnidroid v.9 for the first time, it eventually emerges from lava all hot and burning with a distinct red glow but the moment it reaches for Mr. Incredible with its claws to rip him apart it goes back to metallic gray – otherwise Mr. Incredible’s face would have been slowly burned like a marshmallow over a campfire and that would have traumatized another bunch of children watching the movie which is never good for repeated viewings in the theatre.
Unaddressed Issue: Why does Elastigirl go inside the cramped lavatory in her plane to change her clothes when she is (to her knowledge) the only one aboard?
Unaddressed Issue: How would Gazerbeam, the dead superhero Cyclops knockoff in the cavern, know about Kronos? Similar to Mr. Incredible, he was lured to the island to fight a robot and was probably not given any other information. So why does he know about it? And why does he know it’s so important that he needs to write it down with lasers on a cavernous wall before he died?
Unaddressed Issue: Superheroes get banned in the United States. But what happens with the supervillains? They disappeared too? Because you only need one of them to resurface to make the public want superheroes to come back again. So do we have to assume they all went in hiding after lawyers and politicians got angry at superheroes?