I don't think this is a Yosemite issue, as I saw mentions on the web going back some years. This may actually have been a result of my seat-of-the-pants method of migrating to my new riMac. Nonetheless, in case it helps someone else who's recently updated:
For a few days, Mac App Store has been offering me two small app updates, and won't take no for an answer. I gave it several tries, as these apps are small, but that didn't work. I just ended up with half a dozen instances in the Updates section of these apps in Updates Installed in the Last 30 Days.
Finally, I opened the apps in question. In fact, they weren't updated. So I deleted the apps and another obscure reference to them that Spotlight found lurking in a folder within a folder somewhere deep in the bowels of my riMac.
I made sure Spotlight now found no instances of the app name on my iMac.
Then I updated once again in Mac App Store.
This time, when I opened the apps, I had the latest versions. And after quitting Mac App Store twice, it finally showed no updates available and had no flags in the Apple menu.
Discussion of issues related to OSX 10.10 (Yosemite)
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