Because it does not accept unlimited liability by following DMCA takedown procedure. Following it places Github into the DMCA safe-harbor. Not following it opens Github to liability.

This is what should have happened:

  1. Github is served with a DMCA Takedown notice
  2. Github validates that the notice is valid
  3. Github takes down the $FILE or $REPO
  4. Owner of the Repo contacts Github
  5. Github notifies the owner of the repo that it was a DMCA takedown
  6. Owner of the repo provides Github with the Counter-notice.
  7. Github restores access to the taken down $FILE or $REPO

At this point the party issuing takedown must sue the owner of the repo. It cannot go after Github. It also cannot take down the content again using DMCA to github.