NavMesh is not baked consistently with all GameObjects

Reproduction steps:

1. Open the user's attached project
2. Open Assets > Scenes > Train
3. Select GameObject in the Hierarchy
4. In the Inspector bake new mesh

Expected result: Mesh is not broken
Actual result: Mesh is broken around small cube "Cube_1"

Reproduced with: 2020.3.39f1, 2021.3.9f1, 2022.1.5f1, 2022.2.0b7, 2023.1.0a10

Reproducible on: Windows 11