It seems that stack2nix first tries to clone the master branch for the given repo. This interacts poorly with submodules as they are initialised to the remote on master rather than the given revision.
If the commit you want to use contains submodules which point to a different remote then running stack2nix fails as it can't find the reference.
The way I "fixed" this was to push my branch to the master branch as well but obviously this is not possible in general.