Reproduction steps:

1. Open "Test Bundles.zip" Project
2. Open "Scene1-Loader" scene
3. Enter Play mode
4. Notice that the Blue Cube is stationary (Should be moving up and down)
5. Delete "TestBundleAssembly" Assembly Definition from the "Scripts" folder in the Project window
6. Enter Play Mode

Expected Result: The Blue Cube should be moving with or without an Assembly Definition
Actual Result: Assembly Definition breaks the Asset bundles Blue Cube

Reproduced with: 2018.1.4f1, 2017.4.4f1, 2017.3.2f1, 2017.3.0a1
Did not reproduce on: 2018.3.0a1, 2018.2.0b6, 2018.2.0a1, 2017.2.3f1, 2017.1.4f1 (Assembly Definitions only implemented from 2017.3)

Note:
With Assembly Definitions, Asset Bundles can't find references to scripts