If I'm reading correctly, you have a folder structure setup within an existing project. Then you have those same folders also set up on your extra resource task template to match? That will cause them to be duplicated when the template is attached, if so. The next time you try this process, go into 'Customize and Attach' and unselect the 'Documents' checkbox. It's a little counter-intuitive, but that does affect folders as well.
Workfront doesn't have a way to know that the folder "Contracts" from the original template, and the folder "Contracts" on the ad-hoc task template are meant to be the same. It will assume you want two folders with the same name, and create both. Typically I only put unique folders that need to be created by an ad-hoc template on those, and otherwise let the primary template govern folder set-ups.
