How to reproduce:
1. Open the attached project
2. Open a new scene
3. Find NavigationPoint prefab in the project and drag it to the scene
4. Notice that it has incompatible script
5. Click the prefab Apply button
Result: Fatal Error appears "The file 'MemoryStream' is corrupted!..." and Unity crashes

Reproducible: 5.5.0b9, 5.5.2f1, 5.6.0b10
Not able to reproduce with 5.4.4p4, project crashes because of forward incompatibility. Also it is full of compilation errors

Duplicate of the WON'T FIX case:
The cause of the error is that the users project is not setup correctly, the user has added scripts that derive from ScriptableObject instead of MonoBehaviour to GameObjects, resulting in crashes.. Developer added error to detect this case, so the users can fix the issue themselves.