In the warehouse, Hiro holds a broom as a weapon as he approaches the barrel of microbots, but when he comes closer the broom is nowhere to be found, and there is no sound to indicate that he dropped it.
When Callaghan first meets Hiro, he is seen wearing a blue shirt, but when he asks Hiro for his robot, his sleeve is visibly. In the next full shot of him, his shirt and sleeves are blue again.
In the last shot showing Tadashi's San Fransokyo Ninja cap, the colors of the cap logo "SF" and the "N" are reversed from what was shown earlier in the movie.
During the car chase, the headlights are on, but the tail-lights are not (evident when the brakes are applied). A few moments later, the tail-lights are on.
When Honey meets Hiro, she has earbuds in her ears. She starts talking to Hiro, pulls them out of her ears, and they dangle out of her shirt. The dangling earbuds then disappear in the close-up shot of her and Hiro.
When Baymax scans Hiro the second time, he states that he has no injuries and that the only diagnosis was "puberty". However, the blood pressure reads 113/90 which is considered hypertension (high diastolic blood pressure). Anyone with healthcare knowledge would recognize this as a problem.
The villain's mask is referred to as a Kabuki mask, but it is classical Japanese No theatre that features actors in wooden masks. In Kabuki there aren't any masked actors; the actors' faces are painted in a stylized form.
Cobalt is super toxic, they should all be dead with the amount of exposure they get.
The "District 51" arcade game in Fred's room (based on the arcade game "Area 51") shows a flashing "Game Over" screen every time it shows up. Almost all actual arcade games only display "Game Over" at the end of a game, shortly followed by "attract mode" when the game is trying to get more people to play it. It would be exceedingly strange for an arcade game to display "Game Over" and nothing else for that long.
When Baymax rescues the group from the sinking car, he (it?) should have burst due to the increased air pressure in his (it's?) body as they ascended to the surface.
When Hiro first meets everyone at the college, Honey says her ball of carbide weighs 400 pounds. In reality, a ball of carbide measuring 36" in diameter (judging size from the film) would weigh over 14,000 pounds. This is not necessarily a goof, as it is not stated that the ball of carbide is solid.
When Hiro and Baymax are at the police office, Baymax putting three pieces of tape on each arm and only takes 6 pieces. But when the frame switches, he has a lot more pieces of tape on his hands, arms, and belly. However, an unknown amount of time took place before in that scene, and Baymax could have applied tape then.
After encountering Yokai, Baymax states that he scans the healthcare needs of anyone he meets and therefore has noted the bio-metrics of the villain. Being created in Professor Callaghan's lab, Baymax would have certainly encountered the Professor previously and should have been able to see immediately that the two had identical bio-metrics.
What type of item gets sucked into the portal or not is very inconsistent. Some items are sucked in with great force while similar items in the same shot are not affected. The team hides behind a piece of debris that doesn't seem different from the debris being sucked in to the portal, and not only is it motionless but it seems to shield them from the effects of the portal. They can behave normally without any noticeable force acting on them. Earlier, Hiro was not shielded from the effects of the portal even though he was indoors (he was drawn up against the ceiling by the upward force) and much farther away from the portal.
For such a neat-freak, Wasabi's safety precautions around his laser slicing device in the lab are shockingly weak. Anyone walking through it (which Hiro was about to do) would suffer an instant and incredibly gruesome death, and one could easily lose a finger or a limb by being too careless, yet the only safety precaution is yellow tape on the floor.
The logo for "Project Sparrow" is quite clearly a member of the Apodidae family, probably a swift or swallow.