I have some notes that when deleted from the iPhone app will reappear in my list of notes. I thought this was tied to deleting notes and emptying the trash while I was without signal (on the subway) as they reappeared as soon as I synced again. I have recently also had this happen when I was on WiFi though and deleting a particular note would cause it to disappear for a few seconds and then it would reappear in my list of notes.
The only way I have been able to delete the notes have been to use Notational Velocity. The iPad app is also unable to delete them. There are no tags on any of these notes.