I believe I found a Parsoid issue. Here is a random page to illustrate the issue: https://en.wikipedia.org/wiki/Darreh_Shir,_Chaharmahal_and_Bakhtiari?useparsoid=1. The wikitext contains <ref>{{GEOnet3|-3769380|Darreh Shir}}</ref>. This creates the following HTML:
<span id="mw-reference-text-cite_note-1" class="mw-reference-text"> <span about="#mwt18" typeof="mw:Transclusion" id="mwHg" data-mw="{"parts":[{"template":{"target":{"wt":"GEOnet3","href":"./Template:GEOnet3"},"params":{"1":{"wt":"-3769380"},"2":{"wt":"Darreh Shir"}},"i":0}}]}">Darreh Shir can be found at </span> <a rel="mw:WikiLink" href="//en.wikipedia.org/wiki/GEOnet_Names_Server" title="GEOnet Names Server" about="#mwt18" id="mwHw">GEOnet Names Server</a> <span about="#mwt18" id="mwIA">, at </span> <a rel="mw:ExtLink nofollow" href="http://geonames.nga.mil/namesgaz/" about="#mwt18" class="external text" id="mwIQ">this link</a> <span about="#mwt18" id="mwIg">, by opening the Advanced Search box, entering "-3769380" in the "Unique Feature Id" form, and clicking on "Search Database".</span> </span>
Note where the data-mw that mentions the original template name GEOnet3 is attached. It's attached to the first <span>, as if only that is generated by the template. But this is not true. All <a> and <span> elements in this example are generated by the template. There is either some container element missing where the data-mw should be attached, or it should be attached to the outer <span> instead (however, that is generated by the Cite code).