To reproduce:
1. Open attached project
2. Open "scene1". It contains a sphere that collides with 3 cubes that belong to a parent with a rigidbody
3. Delete/disable the Object2D
4. Enter play mode - the sphere collides with the cubes and prints it's Collision.collider.gameobject in the 2nd line in the console. Notice how it's Cube2 - a cube that the sphere was not touching at any point. The expected result is Cube3