Continuity mistake: At the beginning when Soundwave is attacking the bunker as he ejects his cassettes he says Buzzsaw (the gold condor) but instead ejects Laserbeak (the red condor).
Continuity mistake: Red Alert's door abbreviation has always been an F, then a shield, then a D, but when he is racing through the city when the Autobots are looking for him, he passes them and the abbreviation is: E, shield, D.
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.