Just (bad) story telling... In some episodes of different series it's really excessive and most often there aren't any attempts to explain this at all.
This is especially visible in several episodes of Voyager, considering they usually encounter completely unknown cultures and species. While the universal translator works as an explanation for understanding most aliens, it won't work for written text or displays (after all, they don't have a TARDIS).
Sometimes things like this are explained (at least a bit) either by performed Tricorder scans or at least guesses ("this looks like [techno babble term]") - other times it just happens.
A good example where this is done very well is one of the first Voyager episodes (edit: Time and Again). The crew encounters a planet that has been destroyed just hours before and while investigating Janeway and Paris are thrown back in time by a day or two. They determine this by figuring out the clock/time system used on that planet.
A rather negative example would be multiple episodes where a crew member is kidnapped or somehow forced to use alien technology. It's not always as easy as some kind of weapons with obviously just one or two buttons. Most crew members seem to have a natural talent for modifying alien technology to not only use Starfleet methods and frequencies, but encoding, signing, etc. as well. Seen as a different perspective, this even sounds like some serious breach of the prime directives as well as the disclosure of secret(?) information.