The two samples you provided are from two different files. Can you please ensure that the file doesn't contain carriage return (0x0D) at the server already?
You can do it by `xxd` command if available on the server. Or by downloading using other SFTP tool (e.g. PuTTY's psftp.exe utility, or WinSCP, or FileZilla).
Please note that in SftpTransferType.Binary mode, we do not manipulate transferred data. It is very probable that the carriage return (0x0D) is received in incoming data.