At the end of the Epilogue, it says that after Zero accidentally told Dr. Wily that he would end up killing everyone, Wily decided to never activate Zero and the Cataclysm never happened, causing everyone to go live in Acapulco to avoid a time paradox. So how come Zero is with them in Acapulco in the end? Shouldn't he never have been activated?
Wily probably programmed Zero with fake memories of killing everyone, and then set Zero on a timer to wake up later.
Could be one from a universe where everything went down as normal. Alternatively, just say "I hate time travel" and leave it at that.
Additionally, presuming Bob and George went home at the end, how are they in Acapulco? The early reveal of the Cataclysm shouldn't have affected them, since according to the epilogue they're home and never return.
The epilogue also says everyone died in the cataclysm. I just took that to mean that everything up to that point (including Bob and George never returning) was what would have happened if they hadn't gotten smart.