1. Yes, if not installed properly, although you have to expect a little noise from the closet install, not vibration.
2. I assume the Contractor, both looked where he was going to install the equipment, and installed equipment before? If both answers are yes, then it's his problem to correct. If no, its his own stupid fault. You're going to need more then diplomacy to get him to correct this for the $500.00 you're holding.
Didn't he hear these noises when he fired up the systems?