The reason Nidorina and Nidoqueen can't breed is one of the following:

They choose not to do so in captivity, knowing that it is unsafe for their offspring.

They are just that devoted to protecting their young, and they still lay Eggs but the Day Care Man can't get to them.

Also, in Veilstone's Myth, the young man was afflicted with Nihilego poison, spurring his transformation from an honorable warrior who fought to protect his people and provide food into a zealous slayer of Pokémon who sought glory and power. It has, after all, been established that Ultra Beasts have appeared before.

The reason you can trade between BW and B2W2 is because Bill's Time Capsule technology has become the standard, implemented into the trading systems of every Generation - it's just not outright stated because it's no longer a new thing in-world and most people already know about it.

The reason destructive HMs (Cut and Rock Smash, as well as Whirlpool in Generation II but not IV) are undone is because a well-trained Pokémon will not cause permanent damage if it isn't intended to do so. This is why you need Gym Badges as certification of proper training before you can use those moves - so that you don't actually destroy the environment when you use Pokémon to clear obstacles.

I have some more, but these are the main ones I can think of off the top of my head.