Here's the thing, iCloud has to have a clean master to use, so you need to spend some effort up front to make sure it is.
With MobileMe, I had the opportunity to sync both wirelessly with MobileMe's calendar, and with whatever calendar was in use on my Mac whenever it was plugged in for syncing. It was IMPORTANT to UNCHECK the sync calendar events when connected via USB option, or iOS would read whatever was up on the MobileMe server and display that result, PLUS the iOS device would display whatever calendar events it had updated when it was connected via USB. The result was apparent duplicates, since both the wired and USB synced calendars were displayed. The same was true for Address Book items. So, one or the other option had to be selected, not both.
Now, with iCloud, that server calendar/address book is now the master. Your iOS devices simply display whatever is there. So, you MUST make sure the iCloud items are correct. Then, when they are, turn off iCloud syncing on your iOS devices, then turn iCloud syncing back on. At this point, you get the Merge/Replace option. I'd bite the bullet and choose the option to delete whatever is on your iOS device, and REPLACE it with contents of the iCloud server. I'd do the same on your desktop computers. After that, the server ambiguities go away, and all should be well.
Of course, be sure to back up your contacts, calendars individually, so you have a means to add disconnects back to the iCloud server if something goes awry!
Good Luck!