Summary:
Basically as you duplicate prefabs, they are inserted below the Main Camera instead of the expected location; which is below the instance that you are making a duplicate of.

Reproduces in:
Version: 2020.1.0a19.2305, Revision: trunk f9264fe936e0, Built: Tue, 24 Dec 2019 22:04:49 GMT
Version 2019.3.0f3 (6c9e2bfd6f81), Sat, 07 Dec 2019 14:56:21 GMT, Branch: 2019.3/staging

Does not reproduce in:
Version 2019.2.7f2 (c96f78eb5904), Thu, 26 Sep 2019 18:11:51 GMT, Branch: 2019.2/release

Repro:
1) Create a prefab using a Cube, or a Quad, ect.
2) Create a new Scene
3) Put the new Prefab in the scene such that it is at the bottom of the Hierarchy.
4) Select the Prefab in the Hierarchy Window and Duplicate: Ctrl+D

Result:
> It is inserted below the Main Camera for some reason. Not where I want it.

Expected:
That it works like it used to; the duplicate is inserted the original.

Related Case(?): Duplication of Multiple Objects simitaneously has Regressed (position inside the Hierachy)
https://fogbugz.unity3d.com/f/cases/1210742/