"Destroying object "" is not allowed" error fails in log while working in project.

To repro:
I variant (see first gif):
1. Create a new project.
2. Add new material.
3. Press on the wheel in Inspector -> Edit shader... ->
4. In opened shader press "Compile and show the code". MonoDevelop opens.
5. Return to Unity and press on any object in Hierarchy.

II variant (see second gif):
1. Create a new project.
2. Add a new script.
3. Create an Empty project and attach this script to it.
4. Doubleclick on script name in the Inspector. MonoDevelop opens.
5. Return to Unity and press on any object in Hierarchy.

III variant (see third gif):
1. Create a new project.
2. Create a new Plane.
3. Doubleclick on Mesh (Plane) in MeshFilter or Mesh Collider, or on Element0 (Material) in the Inspector.

Actual behaviour: "Destroying object "" is not allowed" error fails in log.
Expected behaviour: No errors in log.

Does not repro in 5.5, reproduces in 5.6.0b2-4.