On enwiki, the extendedconfirmed right is part of the extendedconfirmed, bot, and sysop user groups.
For some edits made by users in those groups, the user_rights variable does not contain extendedconfirmed
For example:
https://en.wikipedia.org/wiki/Special:AbuseFilter/examine/log/25328598 (extendedconfirmed)
https://en.wikipedia.org/wiki/Special:AbuseFilter/examine/log/25329101 (bot)
https://en.wikipedia.org/wiki/Special:AbuseFilter/examine/log/25321331 (sysop)
The problem doesn't seem to affect all users. For example, user_rights correctly lists extendedconfirmed in these entries:
https://en.wikipedia.org/wiki/Special:AbuseFilter/examine/log/25330403 (extendedconfirmed)
https://en.wikipedia.org/wiki/Special:AbuseFilter/examine/log/25329877 (sysop)