I have some glitches, all caused from using the all TMs and HMs code.
The man that gives you surf stopped me like normal, but I couldn't take surf because I already had it, so I went down the other stairs then he walk onto the stage wanting me to take surf. I went back later and the third time he walks off into the darkness.
The guy that stops you if you don't have surf wouldn't let go to Cianwood even though I had surf and Jasmine told me to go there. I thought about restarting my game, then I learned that the walkthrough walks code I had was wrong, so I jumped the fence and went to Cianwood.
The most dangerous glitch is in Cianwood, the lady that give you fly will keep you in place while trying to give you fly, I had it so she walked though the gym and tried again, soon she walked though the rocks and off screen into the sea. I had to turn the game off and never beat Chuck.
Other glitches:
I never helped get Team Rocket out of Goldenrod city.
If you get Clairs badge the game will think you have all the badges, the same happens with Blue.
I never fought Clair.
The old man guarding the dragons den keeps me from going in.
The boy keeps me from going into Clairs gym.
Lyra keeps me from surfing in New Bark Town.
I never fought Misty, and the machine part event never happened.
Team Rocket is still in thier hideout even though I helped Lance.
Lance was invisible when he gave me whirlpool.
The Goivanni look a like does nothing.
Blue is still on Cinnabar saying that don't have enough badges to fight him even though I beat him already.
Strangely there are three HMs that I'am forced to take, even though I had them already.
They are Whirlpool, Rock Smash, and Rock Climb.