Plugging a tire is not the proper way to repair -- it damages the steel belts under the tread making a proper repair (patch inside the tire) impossible. Also plugs can come out. Also it will void the tire warranty. Some mechanics and dealers will disagree, but after many years I've learned that the ONLY proper way to repair a tire is to remove it from the rim, inspect the interior of the tire, patch from the inside, then remount and rebalance. The brake noise was probably caused by dirt or moisture on the brake disk from removing and remounting the wheel. It is nothing to be concerned about as the brake will clean itself in normal use. A small amount of squealing from disk brakes is normal.
So I took the Prius to the dealership and explained the whole problem. They said that even though I had every warranty, if there is road debris damage...the warranty won't cover it and to contact my insurance provider. Anyways, they did an inspection first instead of replacing the tire. They found a HUGE rusted metal rod (looks like a large drill bit) inside the tire. They found no damage to the car and they said the tire does not need to be replaced. So I'm guessing they checked sidewall/tire damage as well. I asked them to replace the tire anyway but they said that they did not have the specific tire in stock and they recommended not to mix tire brands or models and said that the tire I had was fine. After that, the problem is fixed and I hear NO noise. No wonder, the utility companies dig up the road and it's a real mess....they EVEN LEAVE USED NAILS/DRILL BITS on the road......A BIG hazard. I still have no idea how a long bent metal rod would get inside the tire? The service papers said it was inside the tire.
It punched through the tire when you drove over it. If the original tire repair had been properly done, the service tech would have unmounted your tire and the rod would have been discovered. Using tire plugs is a very bad idea. Tom