A specific case of CheckWiki #104 - "Unbalanced quotes in ref name" is unrecognised by WPCleaner.

If the page contains wikitext <ref name=""> or <ref name="" /> CheckWiki will list it as an error, but WPCleaner will not detect it (Error #104 hasn't been detected in page...). Wikipedia in Croatian (hrwiki) has a bunch of these errors, you're welcome to use it for testing.

Using WPCleaner 2.05b.
Please let me know if you need any additional info.