I've manged to reproduce this bug while writing an article: I've simply copy a reference to reuse it and pasted it at the "wrong" place, in the link label.

How to: on an article already containing references, copy one reference. Then, paste the reference after a link, inside of the blue background that symbolized the link label (the one that I didn't paid attention to).

It looks normal in editing mode:

Even if you select the reference:

But is it not normal when you hover the link or select the label:

And when you save, it is ugly:

[[Lanneuffret|Lanneuffret<ref name=":1" />]]<span class="mw-reflink-text"><nowiki>[2]</nowiki></span>

I've also copied the bad code on my sandbox, which has generated a worse result:

[[Lanneuffret|Lanneuffret<ref name=":1">{{Article|langue=|auteur1=[[Yves-Pascal Castel]]|titre=CAST - Église Saint-Jérôme - Croix de procession, {{s-|XVII}}|périodique=[[Société archéologique du Finistère]]|volume=CXLIV|date=2016|issn=|lire en ligne=|pages=50-55}}</ref>]]<span class="mw-reflink-text"><nowiki>[3]</nowiki></span>[[Undefined|<span class="mw-reflink-text">[2]</span>]][[Croix de procession de Cast#cite note-:1-2|<span class="mw-reflink-text">[2]</span>]]<span class="mw-reflink-text"><nowiki>[2]</nowiki></span>.

It also works for references that are only used once: create the reference somewhere, then cut it and paste it the same way.

If you create a new reference while the blue link label is active the problem (hopefully) doesn't happen.