Most brake pulsation is caused by thickness variation which is a result of adhesive friction material being unevenly deposited on the rotor. For example after hard braking if you keep the car at a complete stop with your foot on the brake a slight amount of pad material will melt onto the rotor causing a high spot. Over torquing or unevenly torquing wheels can cause the rotor to warp especially on cars with aluminum rims. Initially the warping does not cause pulsation but can cause a little bit of a low brake pedal as the pads move side to side in the caliper, but eventually it results in thickness variation and a pulsation. Rotors are not extremely sensitive to warping, tightening the wheels with a torque stick and a properly calibrated impact gun is sufficient.
Here is a link to a good article on thickness variation by carroll smith:
