MR diff sometimes shows wrong old lines and inline diffs

As seen in https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/2568/diffs#diff-13.

The new lines are correct, but the old lines and inline diffs are wrong (but not wrong in the same way)

Old: https://gitlab.com/gitlab-org/gitlab-ce/blob/a93f7099fa2ed98746ebfb5e55322d0afb5068f8/app/controllers/groups_controller.rb

New: https://gitlab.com/gitlab-org/gitlab-ce/blob/575a9d53b0cf36971cd8890086906147b41bd368/app/controllers/groups_controller.rb