AFAICT it has "always" been that way, although I agree it seems redundant.

Reopening to check one thing: this behavior seems at least to be inconsistent.

For instance, in this example the call to RecentTabsUIAdapterDelegate::SetUIAdapter appears only in the "Call Hierarchy" section and the "References" section is not even shown:
https://cs.chromium.org/chromium/src/components/offline_pages/core/recent_tabs/recent_tabs_ui_adapter_delegate.cc?l=69&gs=kythe%253A%252F%252Fchromium%253Flang%253Dc%25252B%25252B%253Fpath%253Dsrc%252Fcomponents%252Foffline_pages%252Fcore%252Frecent_tabs%252Frecent_tabs_ui_adapter_delegate.cc%2523ZV3o8v1d8aqJAJ%25252Bgmb0JId8AgeAE4QqGz%25252Fw6rnLQYGQ%25253D&gsn=SetUIAdapter&ct=xref_usages

Point noted.  Will investigate.

Assigning to flyboy@ in light of comment 3.

Joey, since you've done some work on xrefs, would you perhaps be more familiar with this end of things?

Hmm, I can't repro this (and the example given by Carlos has been deleted).

Marking as WontFix, but Carlos, please re-open if you see the behaviour in #2 again.

It is still happening. Those links needed to be updated:

Updated link from OP: https://cs.chromium.org/chromium/src/content/public/renderer/render_frame.h?l=134&gs=kythe%253A%252F%252Fchromium%253Flang%253Dc%25252B%25252B%253Fpath%253Dsrc%252Fcontent%252Fpublic%252Frenderer%252Frender_frame.h%2523wPPkmencEBo1EC4voUgDf1ZtrZgtla5jgvAgLRcwYrA%25253D&gsn=ShowContextMenu&ct=xref_usages

Updated link from #2 (now using a different example as that file seems to have been removed): https://cs.chromium.org/chromium/src/components/offline_pages/core/downloads/download_ui_adapter_unittest.cc?l=86&gs=kythe%253A%252F%252Fchromium%253Flang%253Dc%25252B%25252B%253Fpath%253Dsrc%252Fcomponents%252Foffline_pages%252Fcore%252Fdownloads%252Fdownload_ui_adapter_unittest.cc%2523N%25252FEhIOKfS1RaApYXIXHP5VxvWiBe7GFu2dkaV1eGEF8%25253D&gsn=SetUIAdapter&ct=xref_usages

I think both of these are WAI. The SetUIAdapter example makes sense to me, since nothing directly references that override of the method. I'm not too familiar with the underlying Kythe model for C++, but this doesn't seem like an unreasonable distinction to make.

In any case, there aren't any xrefs missing from the panel. You can still see all of the callsites regardless of whether they're in References or Call Hierarchy, so if this is a bug it seems like negligible impact to me.