Real life usage showed, that students tend to press the final submission button when they actually want to upload a file. The conclusion is, that this bad usability is caused by bad positioning of the file upload buttons in combination with the primary button coloring of the final submission button, even when no files have been submitted.
One suggestion was to disable the final submission button unless a file has been uploaded. This has the disadvantage that use cases where no document must be submitted (e.g. student handed in physical paper) are not supported anymore.
We decided that we redesigning the particular screen with repositioning the buttons and decorating this with a so-called placeholder panel will make the workflow more apparent. Additional wording and titles have been added as well to make things more clear.