Have reached out to @VirginiaPoundstone Virginia Poundstone at the WMF who is listed as managing API. https://wikimediafoundation.org/role/staff-contractors/#product

Are you reporting that this used to work but no longer does (In which case when was the last time it worked?), or has it always been this way and you are suggesting that the module should be changed to work as you describe?

yes exactly, used to work but no longer works

mdwiki.org runs and older version and it works there

There are no interesting changes between 643fb6c (what mdwiki uses) and current master of TextExtracts. So either its a configuration difference or a change in a different component

So theoretically both mdwiki and en wp should return the same results, BUT

Here is a page on en wp https://en.wikipedia.org/wiki/Wikipedia:VideoWiki/Dengue_fever
and the api en.wikipedia.org/w/api.php?action=query&format=json&prop=extracts&titles=Wikipedia:VideoWiki/Dengue_fever&explaintext=1&exsectionformat=wiki&redirects
only returns === sections, not == or =

The equivalent page on mdwiki is https://mdwiki.org/wiki/Video:Dengue_fever (they are not identical, but both have the three levels of headings)
and the equivalent api call https://mdwiki.org/w/api.php?action=query&format=json&prop=extracts&titles=Video:Dengue_fever&explaintext=1&exsectionformat=wiki&redirects
returns =, == and === sections.

I have made both the EN WP and MDWiki articles exactly the same. And they still return different results via the API.

Further details

1. The API on WP works when the source page is user space or mainspace

https://en.wikipedia.org/w/api.php?action=query&format=json&prop=extracts&titles=User:Doc%20James/Test&explaintext=1&exsectionformat=wiki&redirects

2. But it does not work if it is Wikipedia space

https://en.wikipedia.org/w/api.php?action=query&format=json&prop=extracts&titles=Wikipedia:Dengue&explaintext=1&exsectionformat=wiki&redirects

Same issue exists with Japanese WP https://ja.wikipedia.org/w/api.php?action=query&format=json&prop=extracts&titles=Wikipedia:%E3%83%93%E3%83%87%E3%82%AA%E3%82%A6%E3%82%A3%E3%82%AD/%E7%97%9B%E9%A2%A8&explaintext=1&exsectionformat=wiki&redirects

Okay @Bawolff figured out the issue. It is something called DiscussionTools https://www.mediawiki.org/wiki/Help:DiscussionTools

You can add this functionality to an article, and when this is done it stops working NEWSECTIONLINK

https://en.wikipedia.org/w/index.php?title=User:Doc_James/Test&diff=1222436191&oldid=1222416242

The question is, is their a way to turn it off?

Okay found the answer here https://www.mediawiki.org/wiki/Help:DiscussionTools/Magic_words_and_markup

NOTALK

Stops the tool and fixes the issue with the API

https://en.wikipedia.org/w/api.php?action=query&format=json&prop=extracts&titles=Wikipedia:VideoWiki/Dengue%20fever&explaintext=1&exsectionformat=wiki&redirects

Okay we appear to have this solved...

So what is the solution?

In terms of the solution, you could ask if this is the intended behavior of the extract api, but the workaround is to add the NOTALK to the {{Videowiki}} template. (correct me if I am wrong.)

Change #1048082 had a related patch set uploaded (by Bartosz Dziewoński; author: Bartosz Dziewoński):

[mediawiki/extensions/TextExtracts@master] ExtractFormatter: Rescue headings from being removed

https://gerrit.wikimedia.org/r/1048082

Change #1048082 merged by jenkins-bot:

[mediawiki/extensions/TextExtracts@master] ExtractFormatter: Rescue headings from being removed

https://gerrit.wikimedia.org/r/1048082