That happens for BD or streaming because complex scenes hit the bitrate-per-second cap (VBV maxrate) and quality has to take a hit to fit all the bits in.
If you're working from a source without problems, and they're ending up in the result, Handbrake might be enforcing max rate to hit the H.264 "level" conformance, so "level 5.0" might help. Don't remember if it's got an option for that.
If you're working from a source without problems, and they're ending up in the result, Handbrake might be enforcing max rate to hit the H.264 "level" conformance, so "level 5.0" might help. Don't remember if it's got an option for that.