Dr. Josh Keyes: So what's this about then?
FBI Agent: We don't know. You have higher security clearance than us.
Dr. Josh Keyes: I have security clearance?
FBI Agent: Yes sir, we're just here to take you to your jet.
Dr. Josh Keyes: I have a jet?!
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.
If you look closely with time-frame advance during the pigeon scene you will see a fish "flying" into a window instead of a pigeon.