From wikipedia:
"The term "dark side of the moon" is commonly used poetically to refer to the far side" <--so from a poetic or literary perspective I can accept "dark side" as meaning the far side of the moon, even if it may not be astronomically correct.

But as you said, all moon missions occured on the near side; and the Ark's crash site is shown to be close to Tranquility Base, located on the near side of the moon. So yeah... still don't get why the 3rd Bay film is called "Dark of the Moon."

http://en.wikipedia.org/wiki/Far_side_of_the_Moon