How to reproduce:
1. Open the attached project "1978700_FindRefsInProject.zip"
2. Right mouse click on Assets/TestBehaviour.cs in the Project window
3. Click "Find References In Project"
Expected results: "Test.prefab" is shown in the "Project" tab
Actual results: "Test.prefab" is not shown in the "Project" tab
Reproducible with: 2022.3.52f1, 6000.0.26f1, 6000.1.0a3
Could not test with: 2021.3.45f1 (no "Find References In Project" option)
Reproducible on: Windows 10 22H2
Not reproducible on: No other environment tested
This happens because the index settings in the project is not indexing dependencies.