Plot hole: When the crew's vessel gets stuck in the giant geode and the crystal jams the 'impeller', the magma begins to fill the chamber. They see it melting the crystals, yet they frantically continue working to free the crystal from the impeller and lose a crewman...and yet when they get back in the vessel, the magma indeed melts out the crystal that jammed the impeller. With 2 geologists onboard you would think they'd know that.
Plot hole: When they come up with the idea of setting off the 5 bombs separately, there is a computer screen showing a picture of the Earth and the shock waves starting and interfering with each other. Each shock wave starts off from a different point - they are separated by at least 2000 km. But when they are dropping the bombs, they manage to drop them all within 2 hours (judging by the timer that they set on the first bomb). How did they manage to travel 10000 km in 2 hours?