I was flying around O'Hare today when I noticed several of these holes on the ground. Does anyone know how to fix this?
Not a problem of the airport. It seems you have a 3rd party mesh scenery that has some kind of a problem. Unfortunately, mesh sceneries don't respect the Scenery Library priority, just the resolution so, an higher resolution mesh will always "win" against everything else, regardless of its position in the Scenery Library. Try to selectively turn off every mesh scenery, one at the time, until you find which one is causing the problem.
Also, try different Mesh Resolution settings to see if it makes any difference.