You do kind of expect something simple as a rocker shaft not to have any problems so I totally understand not checking them right away & there's nothing hi tech there, if you have the right blade to take care of it & there's still enough recess for the plug & you clean/deburr it You'll be fine but if they have a toll free # you might see what they say as this is a pretty obvious defect that is preventing your valve cover from fitting & is definitely their mistake.