I don't know what happened on your car but I'll make a couple of observations.
New brakes often do not stop as well as the old ones until the pads and rotors seat in to each other. Depending on the composition of the pads that usually takes about 100 miles or so of driving. Some will seat in with less driving, some will require much more.
Heavy braking on new linings can be harmful to the overall life of the linings. It is usually better to try to avoid heavy braking until they seat in.
Contour and Mystique rotors wear more than most domestic cars but less than most European cars. When first introduced the 95 models often needed new pads at about 30,000 miles. Most of the time the rotors were worn to minimum thickness or less and needed to be replaced at the same time. Ford changed the materials in the pads and possibly the rotors sometime during the 96 model year and the rotors did not wear as bad, but still more than most domestics. The rotors may still be above minimum thickness after turning, but most of the missing material was probably from wear, not from machining.
After replacing the rear pads on my 98 SVT the park brake does not hold the car as well as the factory pads did, even after several months of use. The aftermarket pads (Raybestos semi-metalic) seem to be gentler on the rotors though. I think that once they heat up they stop as well, but they do not hold the park brake as well when cold. The replacement pads are not as noisy as the originals. The cold "squawk" noise from the rear brakes is gone.
In short, there may not have been anything wrong with the brake job. But again, I have not looked at or driven your car, so I can't say for sure. If in doubt, by all means return to the shop and ask them to look things over and road test the car again. Brakes are a safety issue and should be treated by all involved with respect.
