If you have note syncing turned on in your email account on the iPad, Notes will automatically sync with a folder in your email account.
In Mail on an iMac, there is an option to show notes in your Inbox. You can change this behavior by going into Preferences > Accounts > Mailbox Behaviors and unchecking the box. At that point the notes will stay in the Notes folder in Mail. If you delete them or turn off syncing on the iPad, be aware that all those notes will also be removed from the iPad.
That is the only thing I can think of that would cause what you described.