At the safe house Zara was being attacked and then drugged with John supposedly in another room and only after she had been carried out of the building did he appear with a sword to kill the guy who drugged her. If he had had made an appearance earlier she would not have been taken.
After the meeting at the hotel room John is heading towards the car stolen earlier only to be met by the cars owner, John beats the bad guy up and knocks him down the stairs to then be confronted by another bad guy who pulled out a gun. Whilst John was beating up the first guy the second should have shot him then and there.