In The Incredibles, contrary to the poster, Jack-Jack is never shown in the super suit designed by Edna Mode.
The poster/DVD cover for Frozen shows the cast (Anna, Elsa, Olaf, Kristoff, Sven and Hans) standing together and smiling cheerfully, making it look as though the movie as going to be about a team of plucky characters having a fun and magical winter adventure together. The film is actually consistently dark and melancholic, with a several arguments amongst the characters; one of the six, Elsa, is depressed and cruel for much of the movie, and another of the six is actually an outright villain.
The cover of the American DVD of Help! I'm a Fish not only calls it A Fish Tale, it also shows really bad 3D renderings◊ of a few of the characters, (WARNING! The linked image may cause your eyes to bleed!) making it look like a crappy Finding Nemo or Shark Tale rip-off when it's actually a decent, Don Bluth-esque, mostly 2D film. Even weirder, the American cover flatly says "Alan Rickman" above the title (the original cover said "Featuring the voices of Alan Rickman and Terry Jones"), making Rickman seem like the lead role. To make matters worse, Rickman's character isn't even shown on the U.S. cover!
The second Beano video, Beano Videostars, included Roger the Dodger on the original VHS cover, even though he's not on the actual video. Possibly because his checkered jersey made him too hard to animate.
The Brave Little Toaster, probably one of the bleakest kids' films ever made, was marketed as a cheerful adventure and had sugary cover artwork. This goes so far that the screencaps on the back of the VHS/DVD are not even from the film. One of them even showed Toaster high-fiving the Master! (In the film, the fact that they were alive was always kept a secret). The artwork on the back depicts the oh-so-serious waterfall scene, except that the title character has a goofy smile on his face after having made it to the other ledge, waiting for his friends to follow suit! (In truth, they all fell before even the toaster could make it across.) Oddly enough, the original poster showed three screencaps from the film, two from the Nightmare Sequence and one from the dark forest scene.
On the DVD cover of A Boy Named Charlie Brown, Lucy clutches Charlie Brown's arm and stares up at him adoringly. Never mind that her horribly cruel tormenting of him is the whole point of the movie, and that she isn't nice to him for a second...
The 1-disc for Atlantis: The Lost Empire for some reason showed a woman wearing a dress (her left arm is covered by a sleeve). In the actual movie, she wore an outfit that was very revealing throughout most of the film, and she only wore a dress at the end.
For whatever reason, the American release of the dvd for The Painting features a few minor characters who don't even have names. Seen here◊. The spine of the dvd at least has a main character.
Disney's featurette Winnie the Pooh and the Honey Tree shows Piglet and Tigger on the poster, but they don't appear in the film (though Piglet cameos in the opening song). They also had designs that are much closer to the original book illustrations, and they ended up getting redesigned for their appearances in the next short Winnie the Pooh and the Blustery Day.
The notorious Foodfight! has Mrs. Butterworth, the Vlasic stork, Twinkie the Kid, and Charlie Tuna front-and-center on its cover... all of whom are minor characters at best. The actual main character is depicted as a tiny figure in the lower left.