To reproduce:
1. Create a new project.
2. Add an empty GameObject to the hierarchy.
4. Add a ParticleSystem component to that object
5. Drag that object into the Assets folder in the Project tab to make it a prefab.
6. Save your scene
7. Select the object in the hierarchy, and in the Inspector tab, in the ParticleSystem component, open the Shape module.
8. Click the dropdown next to "Shape" and change the value from "Cone" to "Box".
9. Save your scene again.
10. Open your scene file in a text editor, and find the YAML entry for your prefab. It will be the only item with an "m_Modifications:" member, so you can just search for that.
11. Note that in the "m_Modifications" array, there is an entry for the Shape type change you just made, which is expected. It will look something like this:

- target: {fileID: 198299203396264838, guid: cf11313633c9dcb4ca566d1308c037db,
type: 2}
propertyPath: ShapeModule.type
value: 5
objectReference: {fileID: 0}

12. Back in the Unity Editor, reload the open scene by either double clicking it in the Project tab, or using File > Open Scene.
13. Add a new empty GameObject to the hierarchy.
14. Save the scene again.
15. Open the scene file in a text editor again and note that the "m_Modifications" array now has a new entry, which is NOT expected:

- target: {fileID: 198299203396264838, guid: cf11313633c9dcb4ca566d1308c037db,
type: 2}
propertyPath: ShapeModule.radiusThickness
value: 1.0000
objectReference: {fileID: 0}

16. Repeat steps 12-14 again, and note that the "m_Modifications" array has yet another entry for ShapeModule.radiusThickness.
17. Repeat steps 12-14 ad nauseam and watch your scene file grow like crazy!

Reproduced in 2017.1.1p1, 2017.1.1p2, 2017.1.1p3, 2017.1.2f1, 2017.1.3f1, 2017.2.0f3, 2017.2.2f1, 2017.3.0f3, 2018.1.0b9
Not reproduced in 2017.1.1f1, 2017.1.0f3