From the ever-helpful 197.218 at https://www.mediawiki.org/wiki/Topic:U40dlfcwzjtrwmaw :

The automatically generated references may confuse users because it looks so much like the real thing.

Possible solutions

Rename the header to "Generated / Diff references" or something along those lines
Change the styling of the auto reference list
Make the list collapsible / collapsed by default
Add a note to the sidebar indicating that this is solely a "diff reference list"