This phenomena is also often referred to as dark streaks or specks.
Eliminate air traps. To prevent burn marks, move air traps to places which can be vented, or where ejector pins can be added.
Optimize the runner system design. Restrictive sprue, runner, gate, or even part design could cause excessive shear heating that aggravates an already overheated material, causing material degradation.
Modify screw design. Contact material/machine suppliers to get the right screw design information to avoid improper melt mix or overheating that leads to material degradation.
Select machine with smaller shot size.
Optimize melt temperature. Reduce temperature to prevent material degradation from overheating. Note that residual stress may increase when the melt temperature is reduced.
Optimize back pressure, screw rotation speed, or injection speed. Balance shear heat against residual stress.
Solving one problem can often introduce other problems to the injection molding process. Each option hence requires consideration of all relevant aspects of the mold design specification.