Plot hole: Slater decides to render the nuke inert by punching in the wrong code three times. However, when he does this, the nuke becomes armed, and Travolta reveals that he is one step ahead by having used a special kind of circuit board to produce this result. Two questions: One, once Slater has armed one nuke, why not arm them all? You've got nothing to lose, and you can keep Travolta from getting them for whatever evil purpose he has in mind. Slater plans to send them all to the bottom of the copper mine anyway, so just arm them all. Two, Travolta later arms a nuke himself, and then smashes the keypad with his gun. Well, if you can do that, why doesn't Slater just smash all the keypads as soon as he gets the nukes? Travolta would be defeated; movie over.
Plot hole: In the mine shaft, with the lift going the speed it does, it would take over 10 minutes to travel 2000 feet. Yet our characters manage to do it in about two minutes (use the bomb timer for reference). With the bomb timer starting at 30 minutes (not to mention Travolta puts it down to 13 in a later shot), everyone in the mine should be dead before they could escape.
Plot hole: There is no logical reason as to why two pilots on a training exercise would be given classified info such as the access codes for the nukes.