If the rotors were not machined the new linings could be oriented a little differently than the old ones and they're running on top of a ridge of rust. That will wear off in short order. If no high-temperature brake grease was used between the rotor and hub that can cause a crunching noise when cornering. Warped rotors will make the calipers slide back and forth. That can cause a rubbing noise if the caliper mounts weren't lubricated.