Some 8th Gen Civics have had this same problem. I don't believe there should be a hole drilled in your bumper. You could talk with the dealership, but I doubt they'll do anything. It's a bummer they drilled in your bumper.
As far as solutions, here are a couple. Good luck!
DIY Bumper Plugs for .38 cents @Home Depot - 8th Generation Honda Civic Forum
BumperPlugs.com