That's correct, WinSCP lists the remote directory to see if the file already exists, to decide, if resuming a transfer is possible or if overwrite confirmation should be requested.

PUT command issuing an LS or DIR command

while using the WINSCP.com and doing a PUT command, the remote server says that its seeing a directory request being send.

The client is running Windows 2008 R2 with WINSCP version 5.2.0 builds 3157

The Server Iseries OS 6.1