Go to https://en.wikipedia.org/w/index.php?oldid=631438090&veaction=edit
Place the cursor right to the "s" in "Times", and hit the backspace key repeatedly to remove the entire "External links" section including the section heading.
Result: Instead of deleting the section entirely, the following is left in the wikitext: "==<nowiki/>=="
Could not reproduce it in production - If an entire section is deleted via VE, the output will be :
<h2 class="ve-ce-branchNode"><span class="ve-ce-branchNode-slug ve-ce-branchNode-inlineSlug"> <img src="data:image/gif;base64,R0lGODdhAQABAADcACwAAAAAAQABAAA" class="ve-ce-chimera" style="width: 0px; height: 0px;"></span></h2>
No ==<nowiki/>== will be present in Edit source.
I can still reproduce it as described. To clarify, when I wrote "the following is left in the wikitext", I was referring to the wikitext as shown in the preview diff, in the "review your changes" dialog.