Commander John Koenig answers Alan as Tony on his communication device when Alan calls to inform the commander they may have discovered a way to enter the alien structure at around 9 mins. Perhaps Koenig thought it was Tony hailing him on the commlock.
During the crash sequence, when Alan tries to move the floor lever, his hand actually twists to deliberately break it off.
When security shows the crushed commlock to Koenig, you can see that the number pad on the side is just painted on or a decal and not actually buttons like on a normal commlock.
The so-called "thermal laser" is just an ordinary telescope.
The type of brain affliction that Tony is described to have should, at the very least, have been massively and permanently debilitating. That he is already on the road to recovery on the journey back is medically unrealistic as he would almost certainly be in an incurable vegetative state.