This is a very strange event, and it should normally go well if you follow all the steps well. When you have followed the following steps then it should really have to work
Stark Mountain (Japanese: ハードマウンテン Hard Mountain) is home to the
Legendary Pokémon Heatran. The Pokémon is only available on the second
time through the mountain, after revisiting Buck's Grandfather's house
in the Survival Area. Players are required to have Pokémon with
Strength and Rock Smash to proceed through the volcano. After
encountering their rival, players will find Buck, who will travel with
them through the mountain, up to the point where Heatran is
encountered.
Source
How to get to Heatran
- You must first obtain the magma stone which resides deep within the Stark Mountain
- Exit the mountain and go to Buck's grandfather.
- After talking with Buck's father you must return to Stark Mountain and when everything is done well, Heatran should appear.
Handy tips to catch him
- Gather a good lot of powerful Pokeballs such as Ultra balls, Dusk Balls, Quick Balls, Timer balls
- Induce him with a status move (preferably to put him to sleep)
- catch him
If anything is unclear, watch this video
PS
Normally it should work. It can be that you skipped a step and that might be a reason why it isn't there (happens to me often enough ¬.¬)
Good luck catching Heatran
