Along the lines of what Scanialady was suggesting, it could be errors that are being encountered during the FTP transfer itself. e.g. Transfer of a file failed at some point where retrying seems appropriate, but during the retry it now encounters the previous attempt.
Maybe cut-n-paste the Filezilla log area and see if you can find previous attempts to transfer the file that happened before the attempt you had to confirm "overwrite" for, and some error that the previous attempt may have encountered.
In Filezilla settings, also try setting the transfer limit to just one. (Edit, Settings, Transfers, "Maximum simultaneous transfers: 1".) Just to make it a little bit easier on the FTP server, only tracking one outstanding operation from you at a time.