I don't know if this is what the GP experienced, but you can definitely get some inconsistency if you ctrl-C out of Nix while it's in single-user/daemonless mod

I don't know if this is what the GP experienced, but you can definitely get some inconsistency if you ctrl-C out of Nix while it's in single-user/daemonless mode. My sense is that single-user is really only meant as a toy and for use in unprivileged containers— in basically every other situation you want to be talking to the nix-daemon, which maintains proper state and won't get interrupted.