Sphinx will complain about this whether the file is included or not.
However, you can specifically exclude files by using the exclude_patterns config value.
So for your case you might try to change Sphinx's conf.py
file with something like:
exclude_patterns = ['pages/reference-architecture', 'some/other/file.txt']
You can exclude individual files, directories, or use file globbing patterns to match groups of files this way.
EDIT: See: Joakim's answer for another option that was added after this answer was created.