I am having this issue again. I cannot say 100% how to replicate but I can tell you what I am doing.
1. I have 2 tabs open, one of them EverNote and the other is a course I am doing on MongiUni.com so these tabs are not related and certainly not both ever note.
2. I am switching back and forth on Google Chrome taking notes and watch videos and again taking more notes
3. I am in a public cafe with semi-good internet. While it does NOT disconnect, it slows down drastically sometimes and perhaps this is all a network related issue causing ever note to duplicate notes...