Basically, the reason why the waves occur is the universe trying to brute-force "balance" in the grander multiverse. Part of why the waves are able to occur is if said world is unstable. The reason it is unstable is that the world Naofumi is in is actually two. Originally, demi-humans didn't exist in their world until the demi-human dimension merged with the human one, creating the world they are in. So, the amount of time between the waves will increase if they start killing people, and eventually stop if they kill enough. In the case of the L'arc and crew, they didn't want to kill people in their own verse, so they decided to kill the heroes of another and allow that world to die, which will cause a similar effect on a grander scale instead of just a single world.
