With iOS 5, iPhone and iPad users began reporting a new curious behaviour: the label under some apps would occasionally change to read “Cleaning…” Facebook does it; Instapaper does it; Twitter too. It’s a feature of iOS 5 that, to my knowledge, has not been explained.
Since adding iCloud and Wi-Fi sync options, it’s become important to keep app data as clean as possible, so backups are as efficient as possible, so we’re not left waiting around for minutes or hours getting as frustrated as possible.
And yes, this is the same reason that, under the original iOS 5.0, apps like Instapaper would sometimes lose all your locally cached articles. (Since fixed with the addition of a third storage option between documents and cache, one that’s not cleaned but also not backed up.)
There you have it; iOS 5 is just ensuring your iOS device is as lean and efficient as possible.