This is a pretty awesome breakdown of some of the issues:
Also, the entire setup of the movie is heavily flawed.
1) We, the USA, have NEVER landed on the "Dark Side" of the Moon. The time of radio silence is when the orbiter is circling the far side of the Moon. EVERY landing from the US and other nations (manned and unmanned) have been on the "front side" of the moon.
Why? Communication. We don't have geosync satellites around the moon that would allow for constant communication no matter the location. To argue they could have lifted out and re-landed on the moon is beyond preposterous.
Bay is terrible when it comes to actual space travel. He tremendously screwed the pooch on Armageddon (Space Shuttle taking off like a plan on the asteroid??!?!?!) and has done so again here.