To reproduce:
1. Open attached object;
2. Create ScriptableAsset (Assets > Create > Test > Create MyScriptableObject);
-make sure Asset Serialization mode is Force Text (to change it go to Edit > Project Settings > Editor > Asset Serialization > Mode > Force Text)
3. Select MyScriptableObject in the Project Window;
4. Open MyScriptableObject outside of Unity;
5. Edit the value of textString and save the file;
6. Go back to Unity;
7. Notice the MissingReferenceException is thrown in Console window.

Expected result: no MissingReferenceException is thrown.
Actual result: MissingReferenceException is thrown after updating ScriptableObject outside of Unity.

Note: MissingReferenceException is not thrown when you skip Step 3.

Reproduced on versions: 5.3.7p4, 5.4.4p4, 5.5.2f1, 5.6.0b5, 5.6.0b10, 2017.1.0a1.