I use Unity 5.6 on Windows and I have a normal scene with a terrain, rocks and a large plane for water.
When I try select a rock or tree in the scene view by clicking on it directly it always selects the water plane. To select the object I want I have to rotate the camera underneath and then it selects correctly. It’s almost as if Unity is selecting from the bottom first.
I’ve had this issue in many different projects and I couldn’t find anything online regarding it.