Trivia: It seems like a mistake, but it really isn't: Director Nicholas Meyer, in his DVD audio commentary, points out that the time machine should not have stayed in London and rightfully did belong where it ended up - in a museum in San Francisco. This is plausible not because of alternate dimensions or time zones, he explains, but because the machine was crated up and shipped there by museum curators after H.G. Wells' death/disappearance.
Trivia: All three of the children of the real H.G. Wells were still alive at the time of this film's release.
Answer: At the end of the movie, he said that he was going to dismantle the time machine, so it's not used again, thus ending this timeline and the timeline we know as H.G. Wells would come to pass. As for the time machine being in San Francisco, if the machine had never been moved or buried, he would have landed in London.