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.
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.