As Bob gets chewed out in his cubicle by his boss, his pencil holder is centered on his desk. After the boss leaves, it has moved to the edge of his desk, where it falls off and spills pencils all over the floor.
Violet is not wearing the orange headband before the rocket launches but after it appears on her head. There is no way she could have possessed that headband as she was not seen holding it in her hand before the cave scene.
In Mr. Incredible's home office where he has different newspaper articles and magazine covers about him, the Newtropolis Tribune with the headline "Incredible Rescue At Sea" is dated September 14, 2003. This clearly does not fit into the approximate era the movie is set in.
When Syndrome introduces himself to the public, he does so by catching a petrol tanker, which he then flamboyantly tosses behind him and we see a huge explosion. Barely a second later, when the Omnidroid is creeping up on Syndrome, he looks over his shoulder and we briefly see the street behind him, which has no trace of the tanker, or any fiery debris.
When the airplane blows up and Dash, Violet and Helen are falling, once Helen makes herself into a parachute, there is no longer rubble from the plane falling around them and nothing above them. After they are in the water, a big chunk of plane falls almost on top of them.
While the Parr family is fighting the Omnidroid, Mr. Incredible tells Elastic Girl to press the first button of the Omnidroid controller. After telling him to wait, she presses the last button instead the first one.
After Helen catches Bob coming home late from the fire and jewelry store incident, there is a figurine laying on the ground next to the blocks beside Helen's chair. The figurine disappears in the next shot.
After landing in the jewelry store, the rescued fire victims are strewn on the floor around the room. In the next few scenes, these people are no longer on the floor, but they reappear there when the cop draws his gun on them.
In Metroville, when the robot explodes on the water, the upper camera shows Frozone standing behind Helen and on the left side of Mr. Incredible. Then the same scene is shown from the front camera but now Frozone appears at the right side of Mr. Incredible and in front of the whole group.
In the Scene where Mr. Incredible is exercising by lifting railroad cars, the trucks (wheel sets) on each car stay attached when he lifts the cars off the ground. On real railroad cars, the wheel sets are held in place by gravity, so if he lifts the cars, the wheelsets should stay on the ground.
At the end of the dinner fight the ceiling light is stationary, but when Dash opens the door for Lucius the light is swinging and Helen reaches up to stop it. That's because Dash zipped back to his seat after answering the door, and this caused the wind. This is not obvious without close inspection.
The world depicted in the movie has had a very different history than ours. Technology and culture are often much more advanced. Whatever chronology is given regarding music, technology, politics, design, etc., is "true" within the movie.
In the jewelry store after the fire, Frozone gets a drink of water by pulling the lever downward on the water cooler. While bringing the cup up to drink, the lever is still down, meaning there should be water still coming out of it.
The goof item below may give away important plot points.
Bob drives his new black car to the airport for his second trip to Syndrome's island. Later, Helen drives her new red car to the airport to fly Snug's jet to the island. The family uses one of Syndrome's rockets to return to Municiburg, meaning both cars are still at the airport. Yet when the family returns home after defeating the Omnidroid, Helen's car is back in the driveway.