It seems like the notification is not being removed from the notification stack on the iPhone, and probably the iPad as well.
This has been around for a long time and is quite annoying.
It's not specific to iCloud. I'm using Dropbox and the same thing happens. I don't think it has anything to do with syncing. I've also tried creating a task on my Mac, syncing, checking it off, and syncing again. The alert comes up on the iPhone but not the Mac.
It seems that the iPhone version is not removing the alert from the notification stack. This has been going on a long time and is very annoying. Am I missing something?