One problem related to brake loud noise has been reported for the 2006 Toyota Prius. The most recently reported issues are listed below.
While vehicle was in motion on a city street, and also upon back roads, the brakes in my 2006 Toyota Prius seemed to grab. There was also a loud noise upon braking. This issue worsened and the dash lights lit up. I took to local Toyota dealership and it was determined that the brake actuator needs to be replaced due to safety issue of brakes going out in the future. (not if but when). I was told when the brakes go out, I am to push the emergency brake and the vehicle would coast to a stop. This is an unsafe condition and could happen while braking for a red light or braking to avoid hitting a deer. The cost to fix this brake actuator issue will be appx $3000. Upon further research, Toyota knew of the issue and offered an extended warranty that expired Dec 2017. There are several other complaints of this same issue with other '06 Prius owners of this happening before and after the warranty expired in Dec of 2017. This is a safety issue which could cause injury or death when the brakes do stop working and needs to be a recall, not an extended warranty through Toyota that expires.