Howdy there pils,
It sounds like you have updated iMovie to the latest version, but you still see an update for it in the Mac App Store. I would first verify that there is only 1 copy of iMovie in the Applications folder. If so, then I would next delete iMovie with this article:
OS X Yosemite: Install, update, and uninstall apps
Apps downloaded from the Mac App Store: Click the Launchpad icon in the Dock, hold down an app’s icon until all the icons begin to jiggle, then click an app’s delete button . If you later want the app, you can reinstall it from the Mac App Store.
Then re download it from your purchases with this article:
Mac App Store: Finding your purchased apps
That should stop the false update flag from appearing again.
Thank you for using Apple Support Communities.
All the best,
Sterling