Other mistake: When Spike is thrown out of the base by Megatron at the end of the episode, Optimus calls him 'Splik'.
Other mistake: When the Decepticons shoot the monument at the end, Optimus runs to save it, you can see two Optimuses (Most likely because the animators forgot to get rid of the other prime which is just standing there).
The Return of Optimus Prime (1) - S3-E29
Other mistake: When the Protectobots combine into Defensor, his right arm is missing.
Answer: It is whichever ending you want. There is no 'real' set or canon ending to the war. The only semi-resolution is Beast Wars occasionally hints at the Autobots winning (before the Maximal upgrade). However, Beast Wars is a combination of the US cartoon and the US comic, and excludes most of the Japanese continuity. So it is really up to you as to what you want to believe. Most people seem to 'accept' the US universe, ending with Beast Machines.