After being attacked by the masters ship, Jo is in the cage room with the draconian guard, leaning over him and asking if he's alright. Presumably due to editing, in the very next screen she is shown being brought into the same room by Ogrons, with no connecting scene showing how she left the room and was captured.
When the Master first fires at the ship with the Doctor and the Draconian ambassador on it, to missiles are fired from the deployed missile rack. When the Master fire is the third missile, the rack is shown fully loaded instead of having two missiles gone.
Much is made throughout the serial of the Ogrons' utter stupidity yet they can fly a spaceship and use its weapons.