Two reasons for maggots in your soil.
Firstly the manure is not fully rotted which is not a good thing and could affect any plants growing in it. I would be wary of planting anything in manure that is still fresh.
Secondly something has died and is rotting in the soil to attract the flies. This would be the lesser of two evils although not nice to have to dig in.
Is it just in one particular place or all over?