A couple of items. I don't use dynamic folders but have an idea how they work.
Autocrat will not put files in both the dynamic and regular folders.. If you want the dynamic folder, leave the folder blank the first time you are asked for folders
If you want dynamic folders, you need to be using the folder ID which is part of the URL.
You select the merge tag (column) that contains the ID and the files will be sent to the correct folder.
Autocrat does not work with Team drives.
The 4th column added to the sheet by Autocrat contains the status and any error codes. What is in the status column?