I try to upload file from web PHP to shell server and run it with this command (phpseclib)
$sftp->put("$upload", "$imageupload", NET_SFTP_LOCAL_FILE)
You are uploading a text file in Windows format to a Unix server.
Some Unix applications are not able to deal with Windows-style line endings.
The problem is generally resolved using a text mode transfer. But while the text mode transfer is widely supported by FTP clients and servers, it is supported by few SFTP clients and servers. It's definitely not supported by the phpseclib. The phpseclib supports SFTP protocol version 3 only. And the text mode is supported since SFTP protocol version 4 only.
So you need to convert the file to Unix format yourself before the upload.
For a conversion in PHP, see for example: how to convert text file from DOS to Unix line endings?
For more background, see also my article Why are text file line breaks wrong after the file is transferred or edited?