I have noticed in an area with previous resource nodes, i.e. rocks, trees, etc., they still leave a collision box.
For example, let’s say i clear an area of rocks and set a base of foundations (flat surface.) If i then try and place a large crafting station, i.e. wheel of pain or temple, it still registers the rock collision. I get the “Overlapping with an other object or terrain” message. Using the ‘Auto-align object to terrain’ key, when moving the wheel across the flat surface of the foundations it still jumps around like its hitting the ‘ghost’ objects.