Can be anything, from characters not using objects they have on them, to physics not being realistic, or a very big plot hole.
As an example, one of my friends told me that his pet peeve is that in a lot of sci-fi movies, when spaceships run out of fuel, they stop moving, while inertia and lack of atmosphere should keep them in motion.
Is the issue that a neutrino blast wouldn’t have any effect or that one that could disable a ship should also sterilize the contents of that ship?