A trope that's bothered me more and more over the years is planetary chauvinism. So many science fiction settings make the assumption that people will only ever live on planets - and usually specifically Earthlike planets - and anything else is just something for a mining ship to visit, when it's even thought of at all.
A somewhat related issue is the grand importance that Earth always seems to be given. I can understand it from the perspective of writing stuff for the general audience, it's super easy to make them care about whatever's going on by saying "oh no, Earth might be destroyed" but once we're a couple of centuries or millennia into being a spacefaring civilization with colonies all over the place Earth is going to be just one planet out of many. Star Trek is a particularly bad offender here since not only should there be plenty of human colonies just as big and important as Earth at this point but there are dozens of nonhuman Federation members too. The Federation didn't end when Vulcan got destroyed, it shouldn't end if Earth gets destroyed.