Reproduction steps:
1. Create a new project
2. Open Project Settings window (Edit > Project Settings…)
3. Click on Player section and open Other settings foldout
4. Add item to any of the Script Compilations lists by clicking “+” button
5. Remove the item from the list
6. Click on any other section and observe

Actual result: “Do you want to apply changes?” warning pop-up appears
Expected result: Nothing of note happens

Reproducible with: 2021.3.56f1, 2022.3.67f1, 6000.0.58f1, 6000.2.6f1, 6000.3.0b4, 6000.4.0a1

Reproduced on: Ubuntu 24.04, macOS Sequoia 15.6 (Intel)

Note: Issue is not reproducible in Shader Build Settings (Graphics section)