Thanks for your bugreport.

I just tried this on my hardy install and can not reproduce this on a
stock install.  I had a bunch of secuirty updates, selected only
"gnutls" and installed those. After that the icon remained a "security
udpates" needed one.

Could you please run:
$ /usr/lib/update-notifier/apt-check
and attach the output? Could you also please attach your /etc/apt/sources.list

** Changed in: update-manager (Ubuntu)
       Status: New => Incomplete

** Changed in: update-notifier (Ubuntu)
Sourcepackagename: update-manager => update-notifier
   Importance: Undecided => High
     Assignee: (unassigned) => Michael Vogt (mvo)

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update manager notification area icon may be wrong in certain cases
https://bugs.launchpad.net/bugs/239673
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