I upgraded to OS 10.11 which gave me a new version of iPhoto. However, an older version of iPhoto v9.6.1 is stuck in the App Store and I get periodic alerts that it is available for upgrade. When I try to accept the upgrade to hopefully clear it out, I'm told "Update unavailable with this Apple ID".
The app store searches all available drives to update software. You would want to use spotlight to find and delete all copies of that software or set up a privacy to tell spotlight not to index the location where you store an old copy of an app.
Open Spotlight preferences and add an exclusion for the folder containing the app.
Another remote possibility is if spotlight itself is confused / in error - you might need to exclude the entire drive to wipe the bad search results and then remove the exclusion and let spotlight re-build the entire search index for your drive(s).