This is the launchpad, not mission control, and it's only rearranging a few of them: the dictionary app, the system settings app, the app store app, and maybe a few more. So it's not rearranging them by use.
Tried you're suggestion anyways, just for the heck of it.
Didn't work.
One other thing to note, when I first installed Yosemite I was moving apps around in the launchpad, putting them in folders, etc. And in a few instances it created duplicate app icons. I deleted the without a problem, or so it seemed at the time. Not sure if that's related or not.
This is such a strange little glitch, but it's driving me nuts because like I say I do use the launchpad frequently.