The maggots are not harmful to the compost or to any plants, but they are a sign that your soil factory is not working efficiently. They may be the result of either too much bokashi pre-compost in the soil factory, or not enough life in the soil that you put into the soil factory. 
So… you could try putting less bokashi precompost into the soil factory (or put more soil into it instead, to dilute it down). 
And as always, make sure that the soil that you put in there initially is healthy garden soil.  Avoid using store bought soils, as these are sterile and have no life in them.  You NEED life to fuel the breakdown process, and regular garden soil is teeming with it.