There are two SQL queries that should have been run during the upgrade to 3.3.0:
DELETE FROM filters WHERE class_name='plugins.metadata.mods34.filter.Mods34SchemaArticleAdapter';
DELETE FROM filter_groups WHERE symbolic IN ('article=>mods34', 'mods34=>article');
It doesn’t look like these were run in your case, and I’m not sure why, but in any case you should be able to resolve the problem by running them manually in your SQL client.
(Make sure to take a complete backup before running SQL commands manually.)
Regards,
Alec Smecher
Public Knowledge Project Team