For some reason I have badges 1234 and 6! what do I do now where's the 5th gym?
Same thing happened to me in LG. Go to Saffron City, and Challenge Sabrina, the Psychic Type user.
The fifth badge is Marsh Badge you get in Saffron City you have to go to Slipth Co. first and defeat the tower to enter the gym. The Psychic type gym.