See bug report which is reproducible.
I followed the DOM dumping instructions on the debugging page to get the DOM in VE before/after a trivial edit.
I also fetched the data-parsoid for the tid from RESTBase and saved it locally (and edited it to add a "parsoid" wrapper that the Parsoid API expects).
I then ran the following script:
parse.js --html2wt --dump dom:post-dom-diff --selser --pbinfile /tmp/dp --oldhtmlfile /tmp/orig.html --oldtextfile /tmp/wt < /tmp/new.html
Examining the dumped DOM with dom-diff annotations, I indeed find that the <ref> node has marked as having its wrapper modified. I looked at the HTML files and there seems to be some diffs in the DOM nodes. I am stopping here and filing this bug report. I don't know whether this is a VE issue (not sure why the DOM node changed, even if the content is identical), or whether this is an edge case inside Parsoid in terms of its expectations around how <ref> nodes are represented.