I think the level on the crystal means what floor it first appears on after you reached that floor. This also applies on mythstones.
Crystals:
Calcite is level1 meaning it can be found, starting from floor 1+
Angelite is level3 meaning found starting after floor 3+
Quartz is level 6 meaning starting from floor 6+
Diamond is lvl11 meaning found at floor 11+
Larimar is lvl 20. found at floor 20+
Kyanite is lvl30. Found at floor 30+
Sapphire is lvl35: found at floor 35+
Fluorite is lvl40. Found at floor 40+
Emerald is lvl45: Found at floor 45+
Peridot is lvl50: found at floor 50+
Beryl is lvl55: found at floor 55+
Citrine is lvl60: found at floor 60+
Topaz lvl 65: found at floor 65+
Amber lvl70: found at floor 70+
Jasper lvl75: found at floor 75
Zircon lvl80: found at floor 80+
Garnet lvl85: found at floor 85+
Ruby lvl90: found at floor 90+
Amethyst lvl95: found at floor 95+
Obsidian lvl99: found at floor 99+.