I cannot reproduce this.

I can:

Perhaps it's Firefox only?

No, because I also reproduced on Safari on an Air. FTR in the Misc tab of my Prefs there I only have "Floated table of contents" selected.

Im somewhat hopeful T130632 will fix this.

Change 355274 had a related patch set uploaded (by Krinkle; owner: Krinkle):
[mediawiki/extensions/WikidataPageBanner@master] Use ParserOutput::setTOCEnabled instead of OutputPage::enableTOC

https://gerrit.wikimedia.org/r/355274

In T126361#3287295, @Jdlrobson wrote:

Im somewhat hopeful T130632 will fix this.

In T126361#3287353, @gerritbot wrote:

Change 355274 had a related patch set uploaded (by Krinkle; owner: Krinkle):
[mediawiki/extensions/WikidataPageBanner@master] Use ParserOutput::setTOCEnabled instead of OutputPage::enableTOC

https://gerrit.wikimedia.org/r/355274

Indeed. T130632 moves the logic of loading mediawiki.toc from Parser to Skin. It also removes support to toggle TOC via OutputPage. Instead, this should happen via ParserOutput directly (via the same hook). This way it will also be considered by EditPage Preview, Live Preview, and the Parse API –  which is what Parsoid and VisualEditor use.

I can also replicate this now.

The database is locked at the moment, so I can't replicate the bug on labs by importing to https://en.wikivoyage.beta.wmflabs.org/wiki/Tokushima?action=edit
I want to do this before merging the patch.

Change 355274 merged by jenkins-bot:
[mediawiki/extensions/WikidataPageBanner@master] Use ParserOutput::setTOCEnabled instead of OutputPage::enableTOC

https://gerrit.wikimedia.org/r/355274

This still appears to be an issue and I think the issue lies in VisualEditor.
The toc appears in the response from the save API inside visualeditoredit.content
It's possible that either

1. VisualEditor's API is making an assumption about the table of contents being there and adding it itself
2. The VisualEditor response is not honoring the onOutputPageParserOutput hook which can make modifications to the ParserOutput.
3. WikidataPageBanner needs to use another hook provided by VisualEditor

VisualEditor team please advise.

(I can't actually reproduce on that test wiki because apparently the VEdit isn't happening - I'm logged out, and it actually appears in the history, but the Save dialog won't close. Stuff for a different ticket though - T166254)

The fix for this was the same as for mediawiki.toc loading in MobileFrontend and depends on a 5-patch stack in MediaWiki core - which was merged after the branch cut this week, so it'll roll out next week.

Can you reproduce it in beta?

In T126361#3287970, @gerritbot wrote:

Change 355274 merged by jenkins-bot:
[mediawiki/extensions/WikidataPageBanner@master] Use ParserOutput::setTOCEnabled instead of OutputPage::enableTOC

https://gerrit.wikimedia.org/r/355274

@ReleaseTaggerBot added a project: MW-1.30-release-notes (WMF-deploy-2017-05-30_(1.30.0-wmf.3))

Yes. This relates to the HTML not the resource loader module. VisualEditor seems to re-render the page in JavaScript so there's probably still a bug somewhere. Try editing https://en.wikivoyage.beta.wmflabs.org/wiki/Tokushima and following the steps in the description to see this.