nix-index can only index packages on Hydra, but it's not disabling nixpkgs overlays when running nix-env. We don't want overlays as by definition anything added or modified in there isn't going to be built by Hydra, and evaluating packages in overlays can cause indexing failures (in my case a builtins.fetchGit that's only valid on my work computer is blocking nix-index on my home computer). This can be resolved by adding --arg overlays '[]' to the nix-env call.