In one shot, Windcharcger, an Autobot is shown having a red Decepticon symbol.
Starscream also has a red Decepticon ensign in one shot, instead of a purple one.
Right after the fake Optimus Prime destroys the fake Starscream, another Starscream can be seen among the Decepticons. This can't be the original Starscream, as he was on their base at this point.
While the concept of the Autobot Matrix of Leadership hasn't been introduced yet to the cartoon canon (although its idea might have been around when this episode was produced), its absence from Optimus Prime's chest creates an immense continuity error with nearly all Transformers media that came after season 3.
When the real Optimus Prime calls the Autobots back when the clone is leading them to the crevasse, Prime calls out to 'Trailblazer' which should have been 'Trailbreaker'. Got the name wrong.
In their base, when Megatron orders Soundwave to eject Laserbeak to scan Optimus, Soundwave's tape deck on his chest surface is colored blue with the yellow strip around being correct. His tape deck is normally white.
Laserbeak couldn't have scanned Optimus Prime's body from all directions, since he was lying on the ground.
To find out which of the two Optimus Primes is the real one and which is the clone, the Autobots hold a race and a sharp-shooting contest. This doesn't make any sense, since both of them could win with ease, seeing as they have the exact same build. A better solution would have been to test their memories, for example.
The Decepticons have disabled Optimus Prime, who is lying unconscious on the ground. They decide to make a clone of him to infiltrate the Autobot base. Why don't they simply kill or capture him? That way the clone could safely walk into the Autobots' base, and they wouldn't have to worry about the real Optimus showing up to sabotage their plans.
Megatron (when talking through the fake Optimus Prime) misidentifies Ironhide as Bumblebee. In an earlier episode, however, he has proved that he knows the Autobots by their names.
Optimus Prime mispronounces Trailbreaker's name as "Trailblazer" and also calls Spike "Splik". Not his clone who had trouble with names, but the real Optimus Prime.
When Megatron's Optimus Prime clone is born, Soundwave suddenly believes it to be the real thing. This is an unusually ignorant and dumb observation for the otherwise fairly intelligent Soundwave to make, since he witnessed the creation of said clone.