Loud Noisy Brake Pedal on new car?

I have only had my Prius C for 12 days. It has less than 500 miles on it. Tonight on the way home it started making a loud click when I first hit the brake pedal, and then a loud squeak/ pumping (compressing) air sound when I press it down to break. It's not coming from the tires or wheels. It seems to be the pedal itself. The same loud click would happen after I take my foot off the brake. It's very loud, not subtle at all. Is this normal? I am guessing it is not considering it did not happen until today. I will be disappointed if it is because it is quite annoying. I couldn't turn my music up loud enough to cover it. I checked to make sure it wasn't rubbing against anything on the floor when I got out. I also noticed that my battery is not charging over 50%. I drove 20 miles from work to home, braking frequently in the charge zone, so I assumed this should not be the case. This could be coincidence and I am looking for problems because of the noise. I'd take it straight to the dealer if they weren't 2 hours away. Please help. Has anyone else had this issue?