Obviously, it's just a song lyric, but it's not indefensible.
The dark side of the moon is not called "dark" because anyone thought it literally lacked sunlight. "Dark" in this expression means mysterious and unknown, as in "darkest Africa" -- somewhere where the light of understanding does not shine.
Chinese astronomers by the 5th Century AD certainly understood that the Moon was a spherical object phase-locked to the Earth, and therefore had a side that would never be visible from here. Whatever they called it could be translated as "the dark side of the Moon".
There is another question about whether a low-ranking army officer would have used that phrase when talking to (or singing to) a group of recruits, but hey, it's a movie.
"There is no dark side of the Moon. It's all dark."
-- Roger Waters