G'day, I don't know if this is intentional on your part, and I couldn't see anything in the forum or FAQ about it.
It seems the default behaviour when transferring a file is to confirm if you want to overwrite an existing file of the same name. This only seems to work when you are transferring to the "current" directory on the server.
There is the ability to have a list of directories, and if you drag a file to a directory it uploads into that directory, but does not ask if you want to overwrite files there.
I am guessing that your check is done by looking at a local cache of the directory listing, so I thought I'd bring this to your attention, as this "issue" allows overwriting of files without confirmation.