When you set up an iPhone or iPod touch with iPhone OS 3.0 and MobileMe or Microsoft Exchange ActiveSync, you may be presented with a dialog that asks you to merge your contacts or calendars with data already on your device. If you choose not to merge, your MobileMe or Microsoft Exchange data will be kept separate from the other data on your device; this may cause redundant information (for example, multiple copies of the same contact).
You may also see duplicates if you are syncing data with MobileMe or Microsoft Exchange ActiveSync as well as syncing that information through iTunes when your iPhone/iPod touch is connected to your computer by the USB cable.
To confirm you are in this state, while viewing Contacts/Calendars on your iPhone/iPod touch, tap Groups/Calendars in the upper left corner. If you see "On my iPhone/iPod touch" heading, as well as a heading for Exchange or your MobileMe account, your data is being stored multiple times on the device, causing it to appear as duplicates.