I have similar issue which causes some instability sometimes when trying to brake. motors hit minimum several times which I’m pretty sure is causing the problem. it was mentioned in this post Dramatic braking in PosHold and loiter modes and behavior in windy conditions - ArduCopter / Copter 4.4 - ArduPilot Discourse.
I think the quad is overpowered (thrust to weight ratio is high). I was thinking about trying smaller props or adding some weight to the quad or just lower the braking acceleration. Let me know if you found any solution .