There is a case that two same simultaneous connections access the same file.
Before the one connection finishes uploading, second connection downloads the incomplete file and deletes them.

You can prevent this situation by using HiddenStor and HideFiles options if you are using proftpd ftp server.

In your /etc/proftpd.conf ,

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<Global>
  AllowOverwrite                yes
  #slee:using .in.$filename convention and block other connection to download
  #must work with  HideFiles
  HiddenStor on
 
  <Limit ALL SITE_CHMOD>
    AllowAll
  </Limit>
</Global>
 
<Directory /*>
  #HideFiles (\.conf|passwd)$
  HideFiles (\.in.*)$
</Directory>

By defining the correct options, you can effectively block the unfinished uploading files to be shown in the directory listing.