The height of the physical bounding box around the cylinder appears to be misaligned.
Here is playground: https://playground.babylonjs.com/#FA0A45
I made a camera very short in height and left a box from one of my previous topics for easier comparison. You can see that cylinders are flying above the ground. To make it even more obvious you can try to switch between BABYLON.PhysicsShapeType.CYLINDER and BABYLON.PhysicsShapeType.BOX to see the difference.
If you knock down the cylinder to its side it looks normal, if you manage to flip it 180 degrees, it will go partially under the ground. Looks like Havoc makes some offset for cylinder physical bounding box.
I think other PhysicsShapeTypes should be double checked as well.