After defeating the first gym. I went on my PokeGear and went to Badges. The next badge said I needed to go to the volcano. When I did it was Gym 3. Took me like 20 minutes to figure out the badges goes up and down for some reason. So it would be a lot easier if the badges went side by side then up and down. To make things less confusing.
So there was an update released recently that fixed and made the Pokegear so much more usable and helpful. The Pokegear now shows you exactly which city in gym is in as well as what level pokemon will obey you from all the gens. Also, it was updated to remove the weird over level 100 stuff at the further gyms. As far as I know, all it's locations are correct. I've gone through all 7 possible gyms using it. I think you are reading it left to right, which is not correct. Read it top to bottom.. the 2nd gym badge is in the 2nd row of the badges list.
I want them reordered too because on my screen and im sure some iother people have this same problem the text goes off the screen. Please fix this