I think now the references.bib argument can be removed from references.rst:

.. bibliography:: references.bib
    :style: alpha
    :all:

Also, I think :all: isn't necessary anymore, right?

I'm not sure though, because I cannot check it locally because I'm getting some errors (which may be related to my broken installation).

Thanks, references.bib is indeed no longer needed. :all: includes all references, also not cited once. I removed that option as well.
I was able to execute the code locally and found also one wrong citation to Ahrens2012 that was not using the bibtex plugin, and corrected that as well.