Somehow a meteorite was generated underground at height about 50, in Thaumcraft magical biome. I think they shouldn't land like this))

This is intentional.

From the wiki:

Meteorites spawn during world generation on the surface or underground and vary in size. They generally contain a Sky Stone Chest which can contain various ingredients required for advanced technology. You can use a Meteorite Compass to locate meteorites near you and as you explore.