Apparently caused by T247921 // https://gerrit.wikimedia.org/r/c/mediawiki/extensions/Cite/+/1047507 , see Anomie's comment. The update is trivial, but the changes this requires on all wikis doesn't appear to have been discussed/considered during implementation.

It appears like the code highlighted here should have been made part of the Cite codebase years ago, not copy-pasted to 100+ wikis without any change. Maybe I'm missing the point. Why was this done?

I'm very interested in getting bug reports about this area of Cite at the moment since work is active, as you can see, and it's easy to make mistakes when there are such a huge number of combinations of customization being applied. Thank you for taking the time to open a task!

Anomie's comment and suggested solution is correct, the issue was a surprise to me because I hadn't considered the specificity of Common.css rules being lower than the workaround styles we added in the Cite extension.

Of course, updating Common.css across all wikis is a fragile way to do this... We're actively discussing how to proceed in T370027, but for now I'm afraid that the best advice I can give is to add [ style~='mw-Ref' ] to the a element rules for Parsoid refs. This approach has a major advantage of also being forwards-compatible with a potential solution which eliminates the CSS counters entirely.

In T371839#10044834, @thiemowmde wrote:

It appears like the code highlighted here should have been made part of the Cite codebase years ago, not copy-pasted to 100+ wikis without any change. Maybe I'm missing the point. Why was this done?

There is some more context at T156351 and https://www.mediawiki.org/wiki/Parsoid/Parser_Unification/Cite_CSS. @ssastry will remember the details when he's back, but I believe that several wikis actually had changes – e.g. compare https://es.wikipedia.org/wiki/MediaWiki:Common.css#L-144 to https://en.wikipedia.org/wiki/MediaWiki:Common.css#L-89. It may not be a great solution, but there was a reason for it.