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you should delete all partitions on the usb stick and then rerun the LiveUSB tool. You can use the "Disk Utility" tool for this task.

Just select your usbstick on the left side and then remove all partitions on it.

You can also try this method:

su -c 'dd if=Fedora-16-x86_64-Live-Desktop.iso of=/dev/sd''X'' bs=8M'

But be SURE to replace the X with the correct device path /dev/sdX. You can see the device path in the Disk Utility

http://fedoraproject.org/wiki/How_to_create_and_use_Live_USB