The Ultimate Doom: Brainwash (1) - S1-E5
Audio problem: When the Decepticon jets attack the maharaja's palace at the beginning Thundercracker speaks with Skywarp's voice. Later, at their base when the fake Optimus comes out Skywarp speaks with Starscream's voice.
Audio problem: At the end, Inferno comes out from the blaze with Red Alert in his arms, Red Alert then says something, but his mouth doesn't match what he says.
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.