I believe that "Transfer to temporary file name" option is enabled by default for files over 100 KiB. Does it happen for large files only?

I wish to solve the problem from the server side because the users are many, Also I think they don't change anything in the default behavior of Winscp as most of them don't know and just login and work, We downloaded Winscp from a long time, Do you see if we may move to the last version may this helps? I think also to try any alternative and see if the problem will exist or not.
-If I deny users write access to containing folder they will not be able to create new files and they do sometimes. I even tried removing chmod from the users path but still have the problem, Seems Linux changes the permissions using system calls may be and without the need to chmod binary. That will require a search to determine. I thank you for your reply and efforts, Comment please.
Regards,

Have you tried my suggestions?

To freeze permissions deny users write access to containing folder.

I don't think it's a server side problem, I use ACL besides regular permissions, May this causes problems with Winscp? Do you have any idea how to freeze the permissions of files on Linux so normal users can't change it using Winscp?

Either that have Set permissions option set or transfer to temporary file name is taking place. Or it is server-side problem.

I set-up the required permissions on the Linux SFTP server and my users are using Winscp, When they are using or editing the files on the server the permissions of the files are being changed automatically, So when users are calling we can't access the files on the server I login to the server and I find the permissions have been changed, What is in Winscp may change the permissions when viewing or editing files?
Strange behaviour with permissions being changed automatically