In many episodes, the missiles Starscream fires on his arms re-appear after being fired.
In a handful of episodes when the map of the United States is shown on the Autobots' monitor screen, the state of Louisiana is placed inside Texas, and there is a gap where Louisiana should be.
Since the show often recycled their CGI assets, this meant that the jet flown by Agent Fowler has all sorts of robot-bits on it because it used the same animation model as Dreadwing's and Skyquake's jet forms.
The Cybertronians regularly change size when they transform. Most notably, Bulkhead and Arcee have more mass in their robot modes than their vehicle modes. This can be clearly seen when comparing the size of their wheels in robot modes to the human characters beside them.