I knew this was happening, I learned it the hard way, but now I just seen it happening.
So let's say you are creating a container using lxc-copy or lxc-create. The command is running, creating the root directory of the container. But then in the meantime you run lxc-ls -f in some other terminal. Well, I had a script running from the crontab to sample the containers that executed lxc-ls from time to time.
Well, there will be a bunch of errors, missing files, the container fails. You check the files, they are indeed not there. I tried to find the issue for some time when I realized it is the lxc-ls that causes the trouble. And now I saw this:
So the lxc-ls decides the container is not complete and it thinks its mission is to delete the container. Now that's a really BFB (big fat bug). A huge one. Perhaps from the late Carboniferous and early Permian periods.