This is not uncommon and a strip of rubber between bonnet and body should sort it out.
If you have the twist/turn Dzus fasteners then I found the order in which you tighten them made a difference to how easy it was to do. After a lot of trial and error my car mine was to put both pins in the holes on the left side then twist and lock right front, right rear and then the left side could be done in any order!!
