Error "Destroying a GameObject inside a Prefab instance is not allowed" shown when destroying runtime-instantiated GameObject

Reproduction steps:

1. Open the user's attached project
2. Enter Play mode

Expected result: No error in the Console
Actual result: "Destroying a GameObject inside a Prefab instance is not allowed." error in Console

Reproduced with: 2022.2.0a13, 2022.2.0b1, 2023.1.0a3
Not reproduced with: 2020.3.37f1, 2021.3.6f1, 2022.1.9f1, 2022.2.0a12

Reproducible on: macOS 12.4 (Intel)