Replaced brakes and rotors on a 2011 Prius. Runs fine no sounds until you hit the break and you come to a complete stop complete stop and then it grabs and grinds. Did not replace the brake clips on the caliper? I just went with the clips that were there. It only grinds when you come to a complete stop it jerks. Also clean the two bolts on the caliper and re greased them. I did not torque anything. I just tightened everything up.
It's more a clunking noise when you completely stop. Applying the brakes to slow down are just fine no problem.
There's a discussion of this very thing on PriusChat. It might be of some use to you:
https://priuschat.com/threads/clunking-noise-while-braking-please-help.190443/
take a photo of your brakes and maybe we can spot the problem.
Did you do a break-in procedure (series of slow downs from various speeds without completely stopping)?
If it doesn’t improve with use, you may have burned in hot spots on the rotors. In that case you may need to get the rotors turned (most auto parts stores will do it) and reinstall; not an expensive problem, just a hassle.
None of the auto parts stores where I'm at won't turn rotors. AutoZone, Advance Auto Parts, O'reilleys, NAPA, etc.