Well,once we too had driven the Honda City of our friend in about 1-2 feet deep water due to floods(Near Haridwar in September 2011)and although none of the wheel caps were removed but there was a lot of dirt and some small branches etc etc which either trapped in them or simply deformed them.as a result our front right wheel cap got deformed but not removed so maybe due to this dirt or other waste materials flowing in the flood water had done this to your car.This can result in scratches too,just inspect your car once you reach home you will definitely find one or two of them(My Corolla has many of them due to travel on waterlogged ways).
Don't think of anything,just rev the car and reach home,its good that you haven't lost those wheel caps,if you are quite protective(Definitely I am not at all)then you can remove them and put in the boot while returning as we say prevention is better than cure.