I created a new issue, and please bear with my lack of experience on this. 
 I tried my best to create a sample project and give relevant details. 
https://github.com/sphinx-doc/sphinx/issues/3855

Thank you so much for your time, and I apologize for the delay in updating 
this thread. 

Thanks,
Barbara

On Thursday, May 11, 2017 at 10:52:33 AM UTC-5, Komiya Takeshi wrote:
>
> The warning is emitted by Sphinx. So preamble.tex code is not related 
> with the problem. It is caused by only reST notation. 
>
> Thanks, 
> Takeshi KOMIYA 
>
> 2017-05-11 21:35 GMT+09:00 Barbara Pilbin <[email protected] 
> <javascript:>>: 
> > Thank you so much for trying.  It seems like it works for lots of other 
> > people.  It makes me wonder if I have something in my preamble.tex or 
> > config.py doing something I don't know or understand.  I will work on 
> trying 
> > to make something small and shareable.  (When I get something together, 
> I 
> > will submit to the isssues.) 
> > 
> > I truly appreciate your time! 
> > Barbara 
> > 
> > On Thursday, May 11, 2017 at 1:45:30 AM UTC-5, Komiya Takeshi wrote: 
> >> 
> >> Hi Barbara, 
> >> 
> >> I'd tried to reproduce your problem, but I could not. on my local, it 
> >> is able to refer the figures. 
> >> Could you share your project or provide minimal reproducible one? 
> >> If possible, it would be nice if you file this into our issues list. 
> >> https://github.com/sphinx-doc/sphinx/issues 
> >> 
> >> Thanks, 
> >> 
> >> 2017-05-06 4:41 GMT+09:00 Barbara Pilbin <[email protected]>: 
> >> > Hi, 
> >> > 
> >> > I have spent quite a bit of time searching and trying to figure out 
> what 
> >> > I 
> >> > am doing wrong. If anyone happens to see what I have missed, I would 
> >> > appreciate the guidance. 
> >> > 
> >> > Here are the relevant pieces from my conf.py file: 
> >> > 
> >> > # -- Options for automatic Figure numbering 
> >> > numfig = True 
> >> > numfig_secnum_depth = (2) 
> >> > 
> >> > # Add any Sphinx extension module names here, as strings. They can be 
> >> > # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 
> >> > # ones. 
> >> > extensions = ['sphinx.ext.intersphinx', 
> >> >     'sphinx.ext.todo', 
> >> >     'sphinx.ext.ifconfig', 
> >> >     'sphinx.ext.githubpages', 
> >> >     #'rst2pdf.pdfbuilder' 
> >> >     ] 
> >> > 
> >> > 
> >> > latex_engine = 'xelatex' 
> >> > 
> >> > ----------------------------------------- 
> >> > 
> >> > I have a topic file that is trying to reference a figure as follows: 
> >> > 
> >> > ---------- 
> >> > The window displays ( :ref:`fig-authentication` ). 
> >> > The window displays ( :numref:`Figure %s <fig-authentication>` is my 
> >> > caption 
> >> > ). 
> >> > 
> >> > .. _fig-authentication: 
> >> > 
> >> > .. figure:: /_static/access/authentication.jpg 
> >> >    :align: center 
> >> > 
> >> >    Authentication Window 
> >> > 
> >> > ----------- 
> >> > 
> >> > The first sentence outputs the caption of the figure. 
> >> > The second sentence gives me an error that says: 
> >> > WARNING: no number is assigned for figure: fig-authentication 
> >> > 
> >> > In the PDF output, the figures do have numbers assigned to them. 
> >> > 
> >> > I would appreciate any direction that you can provide. 
> >> > 
> >> > Thanks, 
> >> > barbara 
> >> > 
> >> > -- 
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