Nowadays they only bother me when the episode is centered around something that is physically impossible like a certain season three episode.

I even understand why they choose to have sound in space. Just imagine big frakking special effect scenes in space, ships crashing into each other or exploding, and you hear nothing. To the normal viewer, even to the physicists among us, that would be immensely jarring. Just because we know there's no sound in space doesn't mean we'd deal well with being faced with reality on an action/sci-fi TV show.