Yeah, sometimes you have to rely a lot on context to understand if they're talking about Nix the package manager or Nix the language, but the documentation does mostly do it well by strictly saying things like "Nix package manager", "Nix Expression Language", "Nix Packages collection (Nixpkgs)" and "NixOS Linux distribution" so it's mostly clear, I think.
> Packages are built from Nix expressions, which is a simple functional language
> We provide a large set of Nix expressions containing thousands of existing Unix packages, the Nix Packages collection (Nixpkgs).
> NixOS is based on Nix, a purely functional package management system. Nix stores all packages in isolation from each other under paths
> In NixOS, the entire operating system — the kernel, applications, system packages, configuration files, and so on — is built by the Nix package manager from a description in a purely functional build language
Lastly, the learn page (https://nixos.org/learn.html) links to three different manuals in the bottom, titled "Nix Manual", "Nixpkgs Manual" and "NixOS Manual" respectively.
I'm sure if you find specific places in the manuals/guides/wikis where it's unclear which one is being referred to, they would really appreciate your help in fixing it, or at least pointing out it's not clear. They tend to be really responsive in the IRC channel the times I've talked with Nix people.
I do wish the documentation made this division clearer. Currently they’re a bit muddled together.