If you chose the first Smart Copy option that makes an individual copy of the doc for each student, like this:
then the student owns the doc that is now in their folder. Because of this, TD can't automatically delete the doc for you.
(NB: If you chose the 4th option "Share read-write" which shares a doc from the teacher to each student as editors, then the teacher can simply "unshare" the doc.)
You have two options:
1. Ask the students to delete the doc themselves.
2. Use Smart Copy again to over-write the incorrect doc with another doc (i.e. the correct one, or possibly a blank doc) with the same document title. To make sure the old doc is over-written when you Smart Copy again, select "Delete student doc then copy" as below: