Some people have inner editors. I have an inner skeptic. She comes out to play when I try to worldbuild, especially if I'm playing on the science-fictional side of the force.
Me: Huh, I wonder what would happen if we had a crashed-landed alien spaceship, which was carrying a biosphere. A bit like War of the Worlds except on accident and with both us and them getting each other's germs, and their species being all invasive to ecosystems.
Inner Skeptic: Most of the diseases humans can catch from non-humans are either from species we've domesticated or are hella difficult to spread between humans. Why would an alien disease even affect us when there are plenty of diseases that only dogs, for example, get, despite the fact we've been living with dogs for millennia.
Me: There's also things like rabies, which broadly affects anything mammalian. Or protists that are a lot less discriminating about their hosts.
IS: Yes, but we're not talking 'you and your cat'. An alien could be even more different than you and your spider plant on the molecular level.
Me: Or protists that are a lot less discriminating about their hosts. Or I set the story a generation or two in and handwave that bacteria and virii are opportunists.
IS: Also, what are they doing here? Why bother landing on a planet full of natives who have all this history and mythology -- including science fiction -- that tells them that if visitors with advanced technology come calling, the best thing to do is shoot until they stop coming?
Me: Maybe they don't have that history. And we have enough mythology that there'd be confusion as to what they wanted -- look at all the stories that are pretty much 'humans are jerks and lose out because of it'.
IS: Still. You'd have to build in a reason why they'd want to come, given how much every square inch of the planet is owned by someone.
Me: Oceans, especially away from the coasts. Don't point to Europa, since that ocean is under tens of kilometers of ice and the surface is full of radiation trapped by Jupiter's magnetic field. If you're photosynthetic or like to eat life like that, you're shit out of luck.
IS: Why not stay in orbit and resupply from asteroids and comets, and find a better planet? Humans haven't lived on Earth all that long, even relative to the 'air is breathable by us' timeline.
Me: Things are badly broken enough that they need to get as many people down to a stable biosphere as they can.
IS: Convenient timing, isn't it? If these problems had happened in interstellar space, they'd be doomed.
Me: I could invent a conspiracy of people to make sure the ship doesn't leave Earth because they're sick of living on ships. Or invoke 'humans are jerks' and have some who want to kill the aliens and steal their stuff, but they aren't able to seal the deal. Or both. ... Oooh, politics.
IS: But it would ruin your premise of the aliens not being invaders.
Inner Editor: And you still haven't come up with a plot yet.
The thing is, my inner skeptic rarely (if ever) rears her head while I read. And less so for fantasy fiction.