Factual error: At the climax of the movie, when Bond is holding Trevelyan by his foot over the dried lake and the dialog exchange of "For England, James?" "No... for me.", Bond lets go of Trevelyan. He then falls a very long distance onto solid concrete. A short time later, the movie shows Trevelyan still alive and moving his head around. This is not possible. A fall from that that height, especially falling on concrete, would have killed him instantly. The shot of him hitting showed him landing on his head and back first. This would have crushed his skull, and snapped his spine. Even if that didn't kill him, it would have knocked him out cold. The mistake goes even further though. The antenna array then explodes and falls on Trevelyan, while he screams at the top of his lungs. Even if someone was somehow able to survive that fall, the damage done to their body would have caused massive internal damage and bleeding. Trevelyan's lungs would have filled with blood. There is no way he could have screamed, let alone that loudly. So this mistake is twofold. The fall would have killed him instantly. And even if not, he could not have possibly screamed. (01:59:05)
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.
Continuity mistake: Xenia is squeezed to death in a tree. The tree seems to change height. When the helicopter is falling and dragging Xenia, she is lifted up towards a very tall tree. When they look again at her after she dies, the tree is extremely short and her legs are no more than a meter away from the ground. (01:44:00)