Optimus Prime hangs onto dear life when Megatron knocks him off a ledge. He was shown being able to fly a couple of minutes ago.
While Rumble is dueling with Hound underwater, he can also be spotted fighting the other Autobots in the power plant in some shots.
Hound is drawn really small when Spike rescues him and pulls him onto dry land. He seems to be as big as a human, even though he is supposed to be a giant robot.
When the Autobots are standing near the ruby mines of Burma, some of them have drastically miscolored heads.
When Gears transforms, his colors change from blue to light pink during his transformation, and then to red. In the immediate following shot, he is back to being blue.
Hound is teasing Ravage who is locked up in a cage. However because of a big animation error, Hound seems to be inside the cage as well. His animation cell has been placed on top of the cage's cell, not under it.
After Gears transforms, Optimus Prime comes into the shot from behind a mountain. There is a rock in the foreground that covers a portion of Gears, yet Prime's leg (which is behind Gears) can be seen in front of the rock.
Soundwave's lower body vanishes before the Energon in the foreground blocks it from view. Thus, for a moment, he seems to consist of only an upper-body.
During their fight on top of Sherman Dam, Optimus Prime vanishes for a couple of frames, then "pops back" into view.
When Huffer complains that his arm got stuck into the metal frame of the oil platform, his upper arm actually isn't drawn. His forearm is floating in nothing.
When the Autobots introduce themselves to the humans, in one shot, Optimus Prime's eyes keep growing large and shrinking back whenever he looks up due to an animation goof.
A woman can be heard shouting "Thanks, neighbor!" in a man's voice.
When Huffer says "Lets take off!", Brawn's lips are moving.
When Bumblebee hits the ground after the Seekers hit him, there is no sound.
The Transformers use Earth measurements with alien measurements mixed in sometimes.
When Optimus Prime tackles Megatron, the letter orders his comrades to follow him. Not only does this not make sense, it doesn't correspond with his actions. Namely, if he is being hit by Prime, he could not possibly talk so clearly.
The Autobots respond with really surprised faces when Optimus Prime exclaims his pleasure after Ravage (their captive) had escaped. Yet they were the ones who came up with the idea of letting him go in the first place, so there is no explanation for their startled faces. Also in this shot, the car doors on Prowl's shoulders have been miscolored - the colorists probably thought they belonged to the other characters who were standing before him.
If he doesn't need to breathe and can function perfectly underwater, why did Hound put on a protective face-mask when he went after Rumble into the water? In later episodes, none of the Transformers do this.
When Jazz gives the other Autobots the order to transform, he addresses them each by name. Some of them however transform without Jazz saying their names, or are already transformed to begin with.