At the end when the family is back camping, the overhead shot of Maddie shows her wearing the same pink shirt from the first camping scenes. After the shot changes, she is wearing a striped sweater.
Team Sonic watches as Robotnik tracks down location his drones' hacker. In one scene, Tails is wearing his backpack, only to suddenly lose it in the next.
In Japan, Tails had his backpack the whole time but in Robotnik's crab, his backpack disappears.
When Sonic, Tails and Knuckles are chained up by the Robotniks and Shadow. Tails is on Sonic's right and Knuckles is on his left but when they arrive back home to recruit Tom and Maddie for a help with their mission, Tails is on Sonic's left and Knuckles is on his right.
When Shadow attacks Tom (when he was Commander Walters in disguise), Shadow's attack causes a bruise on Tom's head but in the end back at home, Tom's head has no bruise.
The Clock Tower (sometimes called Big Ben) was fully restored by 2021. At the time, the clock's hands and numerals were painted their original blue color.The movie ostensibly takes place in 2024, but the clock's hands and numerals are still portrayed as black.
When Dr. Robotnik is grilling his grandfather Gerald he asks him the value of "the speed of light, divided by the speed of sound, divided by the speed of the bus in the movie Speed". Gerald's answer is roughly correct (depending on the altitude, temperature, and of course medium at which sound speed is defined, as well as the actual average speed of the bus above the minimum required 50mph) BUT the answer is given as 17894 mph while the correct units should be mph^-1.
When Ivo and Gerald Robotnik are dancing through the laser room, their suits protect them from getting hurt by the lasers. However, their heads are completely unprotected by the suits, yet they came out without a single scratch on either of their heads from the hundreds of lasers in the room. Though Ivo does imply that the suits generate thermo-reflective fields which could cover his and Gerald's heads to protect them from the lasers.
At the end of the first movie, Tom and Maddie brought all of Sonic's stuff from his cave to their house. But in this movie, it's revealed that some of his stuff was still in his cave. One of them was his pair of nun-chucks. Though it may be that not all of Sonic's belongings made it all the way to Tom and Maddie's house, as it's likely that some of them got accidentally left behind by Maddie herself in a hurry.
At the end of the second movie, Sonic referred to Tom as Dad. But in this movie, he was still referring to him by his name. Though it may be that Sonic called Tom his Dad just to show that he accepted him as his father, not because it's what to call him from then on.
In Sonic the Hedgehog 2 (2022), Commander Walters states G.U.N was recently formed in response to Sonic's actions in the first film. However, this movie states G.U.N has been established well over fifty years. Though it's likely that Commander Walters was lying about G.U.N. being a new organization and that it was actually being re-established quite recently due to the events of the first film, with only a small fraction of it still active, albeit in secret, since 1974 in order to keep a watchful eye over Shadow on Prison Island.
If Gerald Robotnik is Ivo Robotniks grandfather and the former has been in prison for 50 years and apparently had no children other than Maria then who is Ivo's parent? This has not been answered even though Eggman did ask about who did what with whom and when.
Either Gerald had another child or Maria lived somehow and Shadow wasn't told by anyone. However, Maria is actually also a grandchild, which means that it is much more likely that he had multiple kids.
During the first encounter with Shadow as he is riding the motorbike, there is a scene of a close up of Shadow's hand as he revs the engine of the bike. It shows the throttle to be on the left hand side of the bike when in fact the throttle on motorbikes is on the right hand side.
In the final act when Dr. Robotnik is live streaming his final message to stone, as the camera cuts to the giant screen from the back of stone, a bus suddenly pops up into frame.
In a scene taking place in 1974, the song "End of the Line" by Traveling Wilburys is played on a record player. This song, however, did not exist until its release in 1989.
When Tom (James Marsden) is being carted off in the ambulance, the sound of the ambulance is the American siren, not the English siren.
When Dr. Robotnik is grilling his grandfather Gerald, Dr. Robotnik asks him what the "most elegant formula in mathematics" is, and Gerald replies that it is Euler's identity. However, Gerald mispronounces Euler's name as "yoo-ler," when anyone who considers Euler's identity to be that elegant would surely know that the correct pronunciation is "oy-ler".
Ivo Robotnik refers to a destruction beam taking out all of the 25,000mi radius of the Earth. That figure is the diameter, while the radius from the middle point of the core out to the equator is just under 8,000mi.