HELP! 2007 650i with too many issues!?

HI all - I am hoping someone out there can give me some advice! I took my 650 to Russell BMW yesterday because it was idling rough. The car has about 46,000 miles on it and is still under the Certified Pre Owned warranty. They called me today and said the car needs about $4,000 worth of work. Some highlights are, an air filter, ALL new spark plugs, ignition coils, the bushings are torn, it needs new thrust arms, it needs new control arms! The only thing covered under warranty is the ignition coils. Can someone help me understand, how a car with so few miles can need ALL OF THIS stuff!!?? I have owned BMW's since I was 16, and I have never been so floored! I just put 2 new tires on it at Radial Tire and they mentioned nothing to me. Lastly, shouldn't spark plugs last til 100,000 miles... and if not, there has to be a bigger issue! Please help shed some light on this for me! What should I do?!