Reproduction steps:
1. Open the project from the drive link (ctrl+f "Mon, 12")
2. Open SampleScene
3. Enter Play Mode
4. Inspect the console

Expected result: There are no Shadow Atlas warnings
Actual result: A warning (actually it is a notification type message) "Reduced additional punctual light shadows resolution by 4 to make 6 shadow maps fit in the 2048x2048 shadow atlas..."

Reproducible with: URP 12.0.0 (2021.2.0b4, 2022.1.0a2)
I could not downgrade the project to:
2019.4.29f1, 2020.3.14f1 (says no renderer is assigned, I created a new renderer and pipeline asset, but could not resolve the problem)
2021.1.15f1 (same issue as with 2020.3.14f1, also some input errors are present)

Notes:
1. Everything except the spotlight can be removed in the scene, and the issue will still reproduce
2. I could not recreate this in any other scene
3. Reducing shadow resolution resolves the issue, however, it is not clear why the issue is occurring at this scene in the first place

The warning (notification):
Reduced additional punctual light shadows resolution by 4 to make 6 shadow maps fit in the 2048x2048 shadow atlas. To avoid this, increase shadow atlas size, decrease big shadow resolutions, or reduce the number of shadow maps active in the same frame
UnityEngine.GUIUtility:ProcessEvent (int,intptr,bool&) (at /Users/bokken/buildslave/unity/build/Modules/IMGUI/GUIUtility.cs:189)