I recently experienced this after installing new rotors/pads.
Turns out, the clunk I was hearing when applying the brake pedal was because my pads were too small. I bought cheap brake pads off eBay (no name stuff), and they *seemed* to fit just fine. Then the clunk started. I went to Acura to have them look everything over, and they discovered that the front pads were too small, and were moving when I pushed the brake.
Bought some brand name pads... installed... no more clunk.
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Remove one of your front wheels, and reach your fingers around the pad holder and see if you can wiggle the pad at all. Try to slide it all over the place - front, back, up, down, in, out ... if it moves, that could be your problem.
GL