If you want to just delete one file from a packet, follow the below steps. If you want to delete the entire packet and all of its files, see How to Delete a Packet.
To get to the packet containing the file you wish to delete, you can click My Packets in the Teacher Tools menu on the left.
Find the packet you wish to remove a file from, and click on the file name.
You can also click on the name of the packet, then click Edit Packet, but this is more direct.
Use the Preview to ensure you selected the right PDF to remove, and then click Delete File.
You'll be asked to confirm. If you're sure, click OK.
You'll be redirected to the details page of the packet you deleted the file from. You should see "The file has been deleted" across the top of the page, and it should no longer be listed under Files.