Teacher's have created an assignment and enabled the drop box feature. The students have submitted links to files in their Google Drive. When the teacher uses the "download all assignments" button on the assignment the Google Drive submissions are not there.
When students submit Google Drive Assignments as links, they are just that, links. When you download the files associated with the students' submissions, if they have submitted as a link there is no file to download and there for will not be in your .zip file with other physical files that were submitted.
If you would like to be able to download the files for review and/or annotate within the Application, students must submit their documents as files and not as links.