These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Goddamned Zubats: Averted when they came to Mt. Moon, but only because they skipped the whole cave and went over the mountain instead.
Canon Rape: Lots of it. Almost nothing follows canon. At all. The only thing that's the same is the fact that Pokémon are still what they seem to be, and attacks are still what they appear to be.
At one point, the attacks will actually affect humans the exact same way in which they affect Pokémon. Rachel faints and the judge actually declares her "unable to battle". This was, however, played for laughs.
Lavender Town has a Gym.
The Silph Co. building was historically used as an operating base for Team Rocket, instead of them taking it over.