Not sure what is happening but we need to make sure it is not a bug here before reporting it upstream to sphinx. This is blocking astropy/astropy#11763 .

@larrybradley narrowed down the issue in astropy/astropy#11723 (comment)

I think this is a real issue. I'm getting this same error in photutils. It appears to be due to submodules of submodules:

mod1
    __init__.py  (from mod2 import *)
    mod2
       __init__.py (from a import *)
       a.py (defines myfunc, and __all__ = ['myfunc'])

In this case, Sphinx is now defining duplicate references as:
package.mod1.myfunc and package.mod1.mod2.myfunc and raising the
"duplicate object descriptions".

This started with Sphinx 4 release. Not sure if this was an unintended bug there or if something needs to be fixed in astropy-sphinx for compatiblity with Sphinx 4.