When the Ark is first seen, it's colored silver instead of orange.
When Sideswipe and Sunstreaker get ahead of Optimus Prime after breaking out of the tunnel, both are coloured in Sunstreaker's yellow color scheme for a brief moment.
When the Autobots and Spike board Skyfire, Bumblebee and Spike remain visible for a split second as the door closes behind them, not in front of them as one would expect. They inexplicably disappear in the very next frame, when Skyfire takes off.
When the Decepticons and Insecticons flee from the field, Thundercracker in jet mode is colored in Skyfire's white-and-red palette.
When Sunstreaker and Sideswipe are controlled by Shrapnel, for a couple of seconds Sunstreaker is coloured black instead of yellow.
Right before Kickback, while in the air, kicks into Brawn, he disappears for a couple of frames, and the reappears.
When the Insecticons charge towards the Autobots, Bombshell's Decepticon insignia is blinking from frame to frame.
Early in the episode, just after Megatron & co find the Insecticon's pod, Shrapnell's & Kickback's faces are incorrectly colored black. Kickback's is again colored black in the next scene also.
Skyfire is able to hide in the tall grass, but he's a giant robot, taller than the normal Autobot.
Why do the Decepticons and the Insecticons not know each other if they were all on board their ship, the Nemesis? Even if you assume that there were lots of Decepticons on board and Megatron didn't know them all personally (which in itself is doubtful), the Insecticons must surely know who Megatron is.
Earlier, Optimus Prime couldn't even lift up the framework of an off-shore oil drill, yet in this episode, he manages to lift up a gigantic oil-tanker ship. Granted, he was in the water when he had problems with the framework, but his strength in this episode is almost ridiculous, even compared to later episodes.
That must be one huge tree, with an incredibly strong branch that can hold the weight of all three Insecticons standing on it.