Plot hole: In Cuba, Bond and Natalia are in a plane flying over a lake, attempting to find the Goldeneye control station. The station is hidden, and the Janus Group inside obviously does not want the operation discovered until it's time to go with their plan. They are hidden so well, Bond and Natalia are about to give up. Yet, the enemy fires a rocket at the plane to shoot it down, and sends Xenia in pursuit to finish them off. This does not logically make sense, as the rocket would be a dead giveaway that the base is actually there and lets Bond know it. That, and the rocket would be seen by the US government, letting them know that Janus is there. So even if the rocket succeeds in killing Bond, it would give the US government a precise target and would undermine Janus' entire operation. The logical thing to have done would let Bond leave empty handed. (01:37:00)
Plot hole: When Alec reveals himself to be Janus and that he was alive all that time Alec scolds Bond for re-setting the timer at three minutes instead of six. The problem is if Alec had realised Bond reset the timer on the explosive then he should have had plenty of time to leave the building after Bond escaped, so he shouldn't have been injured.