Reproduction steps:
1. Open the attached project;
2. Open the scene "Scene";
3. Disable an object "Not A Prefab" and clear Console window;
4. Click on "SomeMaterial" in Assets folder and drag it on the object "Prefab With Native Script" in the Scene window (do not drop the material, just keep it on the object);
5. Observe Console window output;
6. Enable an object "Not A Prefab" and disable "Prefab With Native Script", clear Console window;
7. Click on "SomeMaterial" in Assets folder and drag it on the object "Not A Prefab" in the Scene window (do not drop the material, just keep it on the object);
8. Observe Console window output;

Actual result: when the process is done with an object "Not A Prefab", in the Console window you can see that the text becomes longer with letter "a" per frame (NotAPrefab.gif). When the process is done with an object "Prefab With Native Script", in the Console window you can see the same text which is in the Inspector window (PrefabWithNativeScript.gif).

Expected result: the process with "Prefab With Native Script" should act like with "Not A Prefab".

Note: In Edit Mode, an object which is a prefab and has the script "SomeScript" does not update the text when you are dragging the material over it. If you are moving the object, than the text is updated. This is happening just with an instance of a prefab that includes the script. Also, if you drop the material on the object and try drag the same one on the object, everything works correctly. The bug appears just in Edit Mode, if you try to comment it and enter Play mode, everything will be correctly.

Reproduced with: 5.3.6p4, 5.4.4f1, 5.5.0f3, 5.6.0b6, 2018.3.0a7