Continuity mistake: When Hot Rod goes next to Prime and says "Optimus....forgive me," the aerial things on the side of Prime's head are grey instead of blue.
Continuity mistake: When Daniel finds Spike inside Unicron, the control panel he uses to convert his arms to blaster mode is already open and 'active'. Seconds later Daniel opens and then activates the panel even though it was already open to begin with.
Continuity mistake: In the scene where Hot Rod and Kup are stuck underwater, we see Hot Rod fighting a Giant Squid. Just after the Giant Squid swims off we see a shot of Kup lying on the ground with his right arm and his left leg missing. However, when Hot Rod gets to him they have swapped sides, the left arm is missing and the right leg is missing (don't be confused by the fact Hot Rod flipped him). Only two of Kup's parts are missing, as we only see Hot Rod pick up two parts.
Continuity mistake: When Devastator crushes one of the gun turrets, he is suddenly missing his chest Decepticon symbol. (00:17:05)
Continuity mistake: When Prime first transforms (after he says "Megatron must be stopped- no matter the cost") his trailer is missing its Autobot symbol. In the immediate long distance shot that follows, the symbol is visible.
Continuity mistake: During the fight scene between Optimus Prime and Megatron at Autobot City, Megatron pleads for mercy. He reches for a gun that is under some metal. The gun is black in colour. Then Hot Rod jumps on him, Megatron stands up and the gun is now purple. It then goes to a close up of Megatron with the gun in one hand, and Hot Rod in the other, and the gun is now black again. (00:22:00)
Other mistake: When Perceptor pops up to tell Blaster to radio Prime, Blaster acknowledges that Perceptor is there before he even sees him. And I doubt he could of heard Perceptor because of the amount of noise the lasers were making, and Perceptor didn't make any noise. (00:14:45)
Continuity mistake: During Galvatron's attack on the junk planet, you see a glimpse of Shrapnel and Scrapper, who were previously transformed into the Sweeps by Unicron.
Other mistake: When Devastator throws a piece of the wall during the attack on Autobot city, his face is completely blacked out. Looks like they erased it and forgot to draw it back in.
Continuity mistake: When Springer backs away from Wreck Gar at the part where the Junkions attack, Springer is suddenly missing his Autobot symbol.
Answer: The reason for this is the intent of both movies (G.I.Joe and this one) to kill off the old group and bring in a new group for younger kids. You noticed how most of the dead are from the old cartoon. The backlash was so bad that the G.I.Joe movie was changed to not kill off anyone (if you watch it you can see where characters were meant to die but the show was changed at the last sec to keep them alive. If G.I.Joe was release 1st then they would have died and if the same backlash happened you would have seen no-one die in this one.