Revealing mistake: When Sonic and Tails arrive in Green Hills on the biplane, Tom and Maddie are looking up at them, but not focused on the same point. Instead, Maddie is looking to the left, and Tom to the right.
Revealing mistake: During the dance-off scene, when Sonic steps on top of the unconscious guy's stomach, his right foot does not cast any shadows.
Revealing mistake: During the final fight scene while Tom is racing around in the yellow truck, you can see the gear selector is in the highest position the whole time which would indicate the vehicle is in park instead of drive.
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