Downloads or installs?
Downloads you can just continue by downloading the same title again or delete from the install folder in the root of the storage medium you downloaded to.
Installs you need to clear the
/usr/import/ folder of the storage medium you installed to (or just go to system settings -> data management. It should ask you to delete garbage).
//EDIT: Also make sure to reboot after deleting the files as there seems to be an error with the FTP tools.