How to reproduce:
1. Open attached project "PrefabError.zip" and scene "SampleScene"
2. In Hierarchy window, make "CubePrefab" a prefab by dragging it to Project window
3. In Project window, delete the "CubePrefab" (In Hierarchy window, "CubePrefab" turns missing/red)
4. In Hierarchy window, expand the "CubePrefab" object
5. Unchild CylinderChild object by dragging it out (the "CubePrefab" with its children turns gray)
6. Repeat step 2
7. Observe Console window

Expected result: no errors are thrown
Actual result: the following errors are thrown:
AssetImporter is referencing an asset from the previous import. This should not happen.
Assertion failed on expression: '!GetPersistentManager().IsStreamLoaded(metaDataPath)'
Asset import did not unload metadata path. This will leak memory. File a bug with repro steps please. (Assets/Scenes/CubePrefab.prefab)

Reproducible with: 2018.4.16f1, 2019.2.19f1, 2019.3.0f5, 2020.1.17f1
Not reproducible with: 2020.3.0f1 2021.1.0b11, 2021.2.0a8
Not reproducible with: 2017.4 (old prefab system)