In a way, that makes sense. When Mephisto made changes in reality, he had Mary Jane and Peter living lives on different coasts and they both had memories of things that had never really happened. Maybe the memories that Mephisto gave them include a vivid memory of the break-up and Mary Jane moving out, but no memory of why was ever created, leaving both of them angry at each other because, since they have no idea why it happened, it must have been the other person who caused it. If we accept the premise that the devil is going to care about a single marriage because it's the kind of love that only exists once in a hundred years, then it would follow that he'd want to end that love with as much anger and bitterness that he could create because he's the devil and that's what he does.