We asked students in our class to use github to keep all their course project code. Each student created his repo. (I guess I should have created the repo and created teams and it was my mistake). I then forked each of those repos under my organization.
I thought that I could simple pull the changes as and when students update their original repo. I think my understanding of how the pull works is wrong.
In the following image I can see that student has updated his repo with some new documents but is there any way I can simply update the repo I have forked ?

Assuming you have a central repository, you need to update your forked repo, simply add the source repository as a remote and then use a standard git pull. You can then push those changes to your forked repo.
There are two options to easily update your fork:
Option 1
Merge the upstream repo into your own…
Option 2:
Alternatively, you could use rebase to update your fork…
Github has detailed documentation on working with forked repositories: Github: Fork a Repo