I have noticed that on occasion I will use Spread Your Wings, then Fly and I will still take damage as if I am running on the surface I am trying to avoid. For example near the Refuge back entrance just past the ruins where you encounter the waves of Voidkin(?) maggot psychos there is a red bulb, several green bulbs, and a blue bulb all in line obstructing the path to the back entrance. If you cast Fly from just before touching the fire surface you will take fire damage and poison damage during the entire flight which can nearly kill your character.
I notice the bug more if I am standing in a surface > cast Spread Your Wings > Fly out of the surface to a location with an elevation change whether it is above or below my current location. Or if I Fly to the edge of a surface. I can provide a video later if my description isn't very clear.