How can I flag a spam/duplicate application on http://www.apptivate.ms? I can't see any option regarding it.
Now I notify through the Windows 8 developer chat rooms. Is there any way to flag an application there?
For now, stick to reporting them in chat or here on MSO. Don't flag the user's other SO questions. (We are looking into getting a basic flagging system up on Apptivate. Watch this space for the decision.)
This has been implemented. Users with at least 15 rep on Stack Overflow will see a "report this app" link below the left sidebar on every app page. Apps that are spam, dupes, or otherwise need staff attention should be flagged using this link.