falling through terrain but till pivot point touches collider then stops halfway through terrain

My character has its pivot in the centre of body. Now when i apply rigid body and turn on gravity the character falls through the terrain but when the body reaches centre it stops. I have put on box collider and character controller. My character is scaled down to 0.0081. It feels like only pivot is being stopped by terrain collider and not the mesh Of character. why is it doing that. I tried it on cube with collider and it give me same result. i have imported basic water and raised the height of terrain so the water can be lowered. And on the height i have placed a city. When i put my character on a building which has a mesh collider it gived me same results. Stopped as the origin hit the building collider. Body is half way under. Both feet are above the ground and even dropped character from height still same result. Does anybody know what's going on and how can i fix it?