Revealing mistake: When Bumblebee is knocked onto his side, Ratchet kneels down to shove him back onto his wheels. The only problem is that when Bumblebee drives away, the animators forgot to add Ratchet's leg (that was previously obscured) into the frame.
Continuity mistake: Optimus Prime, whose primary color is red, when being tied to a rock alongside his troops during the episode's climax, turns blue for a second.
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.