Deliberate mistake: When the bear pulls Woody into the garbage bin after the other toys have crossed over, his hat is not pulled off when his body is squeezed under the lid when going down. (01:15:35)
Deliberate mistake: When Alice jumps on the dog and they start running, her dress and her hand-band suddenly changed side. Probably they mirrored the image, and instead of going left as directed, it felt more accurate to go right.
Deliberate mistake: There was no possible way for Edith to still be alive after the spiked coffin closed in on her. There are spikes on the doors and at the very back and sides of it, and she couldn't have squeezed in to brace herself. Probably done for obvious reasons, but still a mistake nonetheless.
Deliberate mistake: After the intro, the first shot of Isabel as she starts shouting about not fighting is a flipped shot. Note everything is backwards compared to the following shots. (00:01:15)
Deliberate mistake: When Metro Man flies towards the observatory to save Roxanne, we see a typical "the-characters-see-what-the-audience-sees" shot - a Super-Man-esque shot of him with his arms stretched out in front of him with his fists clenched. This shot is then projected onto a monitor that Minion is watching. It would be impossible to achieve this. It's as if there's some sort of camera on top of the observatory filming Metro Man, which there isn't. We see the observatory enough times to see that there isn't, and even if there was, the angle at which it would need to be at would be impossible to achieve. The shot of Metro Man on the monitor is positioned right in front of him, panning backwards. A camera would need to be very long to achieve this kind of shot, but there simply isn't one present.
Deliberate mistake: When Gale and Lucy see the Blue Star for the first time on the Volcanic island, on the second shot of the beach, the sea and the boat and star, the view from the beach, it is a still picture, the waves are not moving. All of the characters are moving but the sea is perfectly still.
Deliberate mistake: In the scene where Marmaduke runs over Don Towmbly, you can "see" the soft mat where he lands on his face: it wobbles.