How to reproduce:
1. Open attached project "Unity Bug With Dirty Data.zip" and scene "SampleScene"
2. In Hierarchy select "Move Right Prefabbed - Autopopulate"
3. In Inspector check that the "MoveRightAutoPopulate" -> "My RB" value is not null
4. Enter Play mode
5. Observe the red cubes and "MoveRightAutoPopulate" -> "My RB" value

Expected result: all the red cubes are moving and the "My RB" value is not null
Actual result: one of the red cubes is not moving and the "My RB" value is null

Reproducible with: 2017.4.35f1, 2018.4.13f1, 2019.2.14f1, 2019.3.0f1, 2020.1.0a14

Workaround:
In OnValidate method, force to serialize the gameobject with
UnityEditor.EditorUtility.SetDirty(this);