All WinSCP file transfer commands are recursive.

To avoid that see:
https://winscp.net/eng/docs/faq_script_non_recursive

I have a scripth that is set to download all files from a directory on an FTP server. It is also getting all of the files from a subdirectory in that folder. Why is this?

It is a fairly simple script. See below.

option batch on
option confirm off
open GDTFactura
option transfer binary
get *.* c:\reports\factura\input\
exit