How to reproduce:
1. Create new project
2. Add Cube to the Hierarchy
3. Drag it into Project view to make a prefab
4. Add another Cube as child to the Cube prefab in Hierarchy
5. In Inspector Override Apply all changes
6. Observe console

Warnings:
Should not grab hot control with an active capture
UnityEngine.GUIUtility:ProcessEvent (int,intptr,bool&) (at /home/bokken/buildslave/unity/build/Modules/IMGUI/GUIUtility.cs:189)
Should not be capturing when there is a hotcontrol

Reproduced with: 2021.2.0b7, 2022.1
Does not reproduce with: 2021.1, 2021.2.0b6
Note: Reproduces on CentOS7, Ubuntu 20.04