Just ran across this during our run in the mission, during the wolver den in the beginning. It looks like crystals in the give bonus amounts of health, acting as if they were vitapods. The bonus is permanent for the first area, even if crystals are swapped.

We'll test this one again as we finish to see if we can easily recreate it.

Edit: New theory - the crystal may be simply updating the player's health based on the nerf from T1.

Edit 2: Just happened again in 6-1: Plan of Attack, first area.

Edit 3: Also occurred in 6-1: High Temperature Hostages