This seems similar to T199320: CX2: References content is duplicated multiple times when adapted. May be a particular case or a regression.

It seems the underlying problem here is that the reference definition is inside a template (Template Reflist in this case), and Visual Editor does not provide support for those yet (T52896):

In Content translation we can consider marking this as a missing reference when transferred to the translation if there is a way to detect this case.

This bug is really the worst of the ones opened on ContentTranslation in my opinion, given the time spent by all the volunteer contributors who have to go back behind a translation to try and reformat the translations that have been substituted. It literally freezes the citation in a version that can't be edited later, except if somebody spend some time to fill a template. Not good to have such non-editable stuff in our wikis !

It still happens regularly in 2023, I have a script that at least removes unnecessary categories added when substituting citation templates. Check out "untranslated category" ("catégorie non traduite") in my bot's list of recent contributions, ie https://fr.wikipedia.org/w/index.php?title=Rowland_Prothero&diff=prev&oldid=210406768. I can just remove the category shown in red in the article, there is no automatic way to reverse the template substitution (except spend some days with regexes for low success..)

In T213277#9403536, @Framawiki wrote:

This bug is really the worst of the ones opened on ContentTranslation in my opinion [...]

Thanks for sharing your feedback, @Framawiki. As I mentioned above, this issue is caused by a limitation of the editing surface of Visual Editor, which Content Translation is using. I copied your feedback in the ticket where the Visual Editor issue is captured: T52896: VisualEditor: Support editing citations defined within a template