The problem is with our html conversion of nodes as explained in screenshot.

The boolean parameter of ve.dm.converter.getDomFromNode indicates whether the content is for clipboard or not. Setting clipboard mode helps to have the reference body resolved and inlined in each paragraph. But if we do the same for reflist , there are consequences. One issue is the reflist template wrapping goes away and mw:Extension/references remains. This is the root cause of this ticket.

We don't look at the content of reflist template or references - we don't machine translate the content inside it. We also don't adapt the items inside it. So we don't need to set clipboard mode true.

Change 506112 had a related patch set uploaded (by Santhosh; owner: Santhosh):
[mediawiki/extensions/ContentTranslation@master] Do not use clipboard mode to get HTML of reference list node

https://gerrit.wikimedia.org/r/506112

Change 506112 merged by jenkins-bot:
[mediawiki/extensions/ContentTranslation@master] Do not use clipboard mode to get HTML of reference list node

https://gerrit.wikimedia.org/r/506112

The query https://quarry.wmflabs.org/query/33366 fails with Unknown column 'rev_user' in 'where clause'.
As far as I could see, the rev_user exists only in the following tables.

SELECT distinct(TABLE_NAME) FROM INFORMATION_SCHEMA.COLUMNS WHERE column_name like 'rev_user%'\G
*************************** 1. row ***************************
TABLE_NAME: flow_revision
*************************** 2. row ***************************
TABLE_NAME: revision
*************************** 3. row ***************************
TABLE_NAME: ep_revisions
3 rows in set, 13 warnings (0.23 sec)