To reproduce:
1. Open the attached project
2. Open the "Main" scene located in the "Scenes" folder
3. Make sure the project is targeting WebGL
4. Make sure you aren't in play mode
5. Make a change to the list of strings on the "TestPrefab" object in the "Prefabs" folder
6. Delete the "test-bundle" asset bundle and manifest from the "WebGL" folder in streaming assets
7. Select "Build AssetBundles" from the AssetBundle drop-down in the toolbar
8. Hit play and select the instantiated "TestPrefab(Clone)"
9. Repeat steps 4-8. Note that the prefab loaded from the bundle will not reflect the values of the prefab that was bundled.

Reproduced in 2017.2.0b2, 2017.2.1p1, 2018.1.0b1