We moved an application from an 853 server to a 9.01 server and users reported that multiple attachments were being uploaded into the XPages attachment control.
It seems to be related to this bug in 9.01
LO82247: PARTIAL REFRESH OF A DIFFERENT PORTION OF AN XPAGE CAUSES THE CONTENT OF A FILE UPLOAD CONTROL TO DUPLICATE.
Which has been closed with no resolution to be fixed in a future release.
So I have had to

  1. Open a ticket here
  2. Identify the issue
  3. Remove partial refreshes which has a negative impact on uasability
  4. Test the “fix”
  5. Submit the change to source control
  6. Deploy the fix to the server
  7. Inform the users that a workaround has been put in place while IBM fix the bug
  8. Then in the future reverse steps 3,4,5,6,7

This is not a sustainable way to work.