Fridge Logic: The lake is filled with sulphuric acid, so corrosive it even starts eating through the boat's hull. And yet, the dead fish floating on the surface are all perfectly intact... Though it has to be granted that it's probably a kind of meta-Gory Discretion Shot (as it's a PG-13 film and dissolved or half-corroded fish bits would probably be a little too over the top), but it's still grating when they otherwise try to be decent with the science.
Fridge Horror: Towards the end of the movie, after Harry Dalton is kicking the E.L.F to get it to respond, it cuts to the other volcanologists and one of them (the one who realizes that it's a signal Harry's alive) asks how long the light has been blinking. The other fellow responds "A day or two". Think about that for a minute. We saw the exact moment the E.L.F started working and then it cuts to two days later. Harry has been stuck in the almost-completely crushed cab of a truck, buried alive inside an abandoned, collapsed mineshaft, with no food, water, or room to move, not knowing if Rachel and the kids are alive (all this on top of a shattered arm bone) for TWO DAYS. And then you have to tack on the time it would have taken to pinpoint the signal and stabilize the shaft enough to get him out. It's a wonder he didn't go flat-out insane by the time he was rescued...
A case of Art imitating life in this case, as earthquake victims have been rescued from being trapped for DAYS under the rubble of the buildings that fell on them. In some cases, rescuers have gone so far as to write them off the moment they find them... only get a big shock when the corpse moves and calls to them to get him/her out of there.
What kind of scientist sees a light blinking on a monitoring machine and clearly doesn't know what it means, and for two days doesn't ask anyone about it?