Code of Hero - S2-E9
Continuity mistake: When the Maximals are disintegrating Dinobot's remains, Rattrap can be seen in his original form when he should be transmetal.
Coming of the Fuzors (2) - S2-E3
Continuity mistake: During the battle at the beginning there is a shot of Tarantulas and Waspinator appearing with Megatron commenting on how reinforcements have arrived implying that they had just got there. The problem is, the previous episode already established them as having arrived before the battle had begun, and they had even been shown fighting before their suppossed "arrival" mid battle.
Plot hole: Series 2, Episode 11, The Agenda (1). The Tripredacus Council explains that Ravage will be able to find Megatron and the others by tracing the transwarp wavefront back through time to its source. If he truly did follow it back to when it started he would have arrived moments after Optimus destroyed the alien weapon in "Other Voices: Part Two" which created it, yet he arrives considerably farther in the future.
Factual error: Megatron tells Ravage that the Golden Disc was launched aboard the Voyager spacecraft, just as the Great War between Autobots and Decepticons began. Either Megatron is wrong or Cybertonian history is wrong, because Voyager was launched in 1977, and the Great War didn't begin until 1984 (the first season of The Transformers), seven years later. The disc can be read by lasers, but it was in fact an analog recording (as digital recording did not exist until the early 1980s with the compact disc). Just as well, the disc was only twelve inches wide; it looks much bigger in Beast Wars.
Chosen answer: Terrorsaur was probably removed because his character was far overshadowed by Tarantulas. Both characters were treacherous and backstabbing towards Megatron, but it wouldn't have made sense to have two characters who served the same purpose, story-wise. Scorponok was removed because they wanted to introduce Quickstrike, and it wouldn't have made sense to have two scorpion characters on the show.