Being that you have beaten all the gyms in the Lauren league, I suppose the you are trying to catch all the legendaries, and Heatran is in Mt. Vulcan. 

This game is very much known for the glitches. I have also had the same exact experience...I went to go get myself Heatran, but the trainer was there, even though I did have the Repels and such. 

The same thing also happened when going through the cave where you fight Zero( or maybe Percy? I forgot). There was a part of the cave that was closed because Team Steam Grunts were blocking the way, and the only way to get past them was to defeat Zero (or Percy?). I did just that, and so I got past them. But going back into the cave, having already beaten Zero (Percy), the grunts were still there. I went back up to see if I Zero (Percy) was there, ad apparently, I had to fight him again to pass through. This was when I beat all gym leaders in both regions, and was just hunting for legendaries. 

Many glitches involve replaying certain parts of the story that you already have completed, which is kinda annoying, seeing how some events can only be passed once, especially with your case. I do not think the Professor is on the street, so you cannot battle her again to make the replayed story go on.

BradHawk :

The only way to handle this is to keep restarting the game (like refreshing and such). I had to do that multiple times, and even wait a few days until (most) things were back to normal. 

You can restart the game itself, all the way back to the beginning, but it will not guarantee a glitch-free game. Glitches will most likely happen again, and will be a tremendous pain in the rear.  

By the look of things, you basically finished the game. There's the Lauren Elite Four and the World Championship, and that's pretty much it. Glitches won't stop you, especially since you seem to be having a glitch with trying to get Heatran. Heatran is a totally an optional Pokemon to get, for he really doesn't serve much help in the game (since you get him late). The E4 and W.C> are totally passable without Heatran, so don't concern yourself too much with him.