Tested v0.5.1 on several epubs and the only issue I ran into was after using calibre's ModifyePub plugin to add a cover image. This adds a line in the cover xhtml file reading:
Code:
<meta content="true" name="calibre:cover"/>
When
Remove all iss and associated links is checked, CustomCleanerPlus removes the 'name="calibre:cover"' which caused epubcheck to flag that line as an error.