If it a theme (.thmx) or a template (.potx)?

Usually the problem is caused by the author adding images or shapes directly onto layouts.

PowerPoint automatically marks these as userDrawn='1' in the XML. It interprets this as the user really really wants to retain this item and then thinks of silly ways to achieve this (like duplicate masters). There is no way to prevent PowerPoint marking them as userDrawn but you can (with difficulty) delete it.

If you know how to edit the XML for the layouts search for userDrawn="1" and either delete or change to ="0". Don't do this (or at least use a copy) if your XML skills are poor because XML is not forgiving of mistakes.

__________________
Microsoft PowerPoint MVP 2007-2023
Free Advanced PowerPoint Tips and Tutorials