Which logs did you check? If you only checked your access_logs and nothing was in there, then that means they didn't use the software to upload the file and so they must have done this directly via your server.
When you connect with SSH, it instantly uses the command "sftp", which calls for the SFTP software to transfer files, basically like FTP. The Shell logs (messages & secure) only shows commands, not what happens inside the software. & sftp-server never showed any logs.