When uploading, I always see an error "file not found."
BPFTP checks to see if a file already exists before uploading, so it can be resumed if necessary. If it doesn't exist then you'll get this error, which can be ignored. If you never intend to resume uploads and you're using v1.08 or later then go to options|toggles within BPFTP and disable "check filesize on upload", this will also speed up the upload process slightly.