Flies should find it rather difficult to get into your Wormery, but if you find flies (or in some cases maggots) in your Wormery, it's usually because it's too wet. The wetness itself is usually caused by exposing the Wormery to rain and/or putting food in that's too wet.
If you do end up having a problem with flies you can use an organic fly spray to kill their life cycle. Alternatively, you can put in a sticky fly trap to remove them as a temporary measure or, better still, use citronella products which will make your Wormery very resistant to flies due to the scent it gives off. The citronella is also non-toxic.
Instructions on how to deal with this are provided in the instruction booklet.