Continuity mistake: After Sonic runs by the radar gun the first time, triggering it to show a 296, Tom picks the radar gun up and looks at it. In the view of the radar gun, he lifts it and has it tilted to the left of himself, left of screen in this shot. When it cuts to a front angle showing his face, the radar gun is now tilted to point to his right, which is now still left of screen. (00:04:49)
Continuity mistake: As the Echidnas first start attacking Sonic and Longclaw, she slams the door shut quickly to catch the arrows shot at them. The In the close up of the door from the outside, the arrows are in a different pattern and are closer together than the holes when seen from inside that are a bit more spread out. (00:02:23)
Continuity mistake: During the chase scene with Robotnik's robotic vehicle, at one point an EMP device is launched which misses Tom and Sonic's pickup truck and instead latches onto a minivan in front of it. Except just a few shots prior, there was a wideshot of the road, and you can see that Tom's pickup truck and the robotic vehicle were the only cars on the road. The minivan just sort-of... appears.
Continuity mistake: At the beginning of the movie, we see a portion of the climax where Robotnik is chasing Sonic. At one point in the very first shot, he runs up the side of a building, onto the roof, then back down. However, when we see the complete chase at the end of the film, he never runs up that building.
Continuity mistake: At the start of the film, Eggman is chasing Sonic through the streets and there is a shot of the city skyline down a street behind Sonic as he makes a turn. The camera then cuts to inside Eggman's ship to a close up him with the city skyline still behind him, only now it's different buildings behind Eggman. (00:01:00)