If layer's camera has x,y, and z-rotation, picking isn't accurate.
To repro, add some objects to a layer and modify layer's camera so that it has x rotation of 45, y rotation of 45, and z rotation of 90. Clicking on the objects on the scene view doesn't select them anymore accurately, especially if the object is towards the edge of the scene.
Widget arrows in particular are practically impossible to pick.
The actual issue is likely in the runtime2 rather than the editor.