Plot hole: When John has Yuri pinned to the uranium boxes, Yuri reaches into his coat and turns on his walkie talkie so his daughter and minions can hear. John McClane doesn't notice and he is right there. There are two things wrong with this. We hear the beep the radio makes when it is turned on, and it was loud enough that John and Jack would have easily noticed. But even if they didn't hear it, there is another issue. John is a New York cop, or even a detective. As such, he would have extensive training for dealing with armed men, and he would have noticed Yuri reaching into his coat. Even if he didn't hear the radio beep, he would have stopped Yuri's hand or done something, assuming Yuri was reaching for a gun.
Plot hole: When Jack and John are on their knees in the hotel, with their hands zip-tied behind, Jack manages to use a hidden knife to cut his bindings and starts kicking bad guy butt. Jack immediately joins the fray but a careful review shows that at no point did John use his knife to free Jack.