Time Machine has repeatedly and silently added both my Boot and Master volumes to its “Exclude these items...” list.
This is not a one-time thing, I have seen it happen 15-20 times in 3 months. This includes after erasing the backup drive and the original volumes, so it is not tied to a particular volume; it is a general bug. With OS X Lion and Mountain Lion.
I never saw this bug when I was using Leopard or Snow Leopard. With Lion, I stopped using Time Machine as it was severely slowing down my system and frequently corrupting its backups.