Other mistake: When Robotnik, Stone, and Knuckles are eavesdropping on Sonic and Donut Lord's text conversation, the third text is supposed to be from Sonic but it appears as Donut Lord's text, on the wrong side of the conversation. (00:40:00)
Continuity mistake: When Tom and Maddie go to check on Tails when he tries to get up on the beach to help Sonic, the scenes are cut badly and show Maddie leaning down two times.
Continuity mistake: When Knuckles and Sonic are on the beach, they are sitting side by side by the pile of sand, but when Sonic sees Tails and turns back to look at Knuckles, Knuckles is sitting much further away.
Continuity mistake: Towards the end of the movie, after the baseball game they go to the blue Chevy truck. One scene shows the blue truck with wheels from a Toyota Tacoma, then seconds later shows a different set of wheels on it.
Continuity mistake: In the beginning scene, Sonic is stopping the armored car robbery. To stop the armored car from crashing into the ice cream shop, he takes a drill he sees on the floor to take apart the armored car. The drill has a round hex head bit. When he gets on top of the car, the screws are Phillips head screws.
Answer: Because Robotnik was betraying him. Dr. Robotnik promised to help Knuckles get the Master Emerald, so they could use it to defeat Sonic. But Robotnik was using him all along because he wanted the Master Emerald for himself... he never actually cared about Knuckles and never intended to help him get the Emerald. Thus, Knuckles is shocked and says that Robotnik taking the Emerald for himself was not part of their deal.
TedStixon