Mountains are higher than the atmosphere?
This is a bit of a gray area, as an atmosphere doesn't have a clear boundary. That being said, Olympus Mons on Mars is so tall, the atmospheric pressure on top of it is only 12% the average pressure on the surface of Mars. That's near vacuum by terrestrial standards.

https://en.wikipedia.org/wiki/Olympus_Mons#Description

In general, for this to happen you need:


a pretty thin atmosphere to begin with
some exceptional geology that ends up producing very tall anomalies like Olympus


It's not a very likely combination, but it can happen, as seen on Mars.