Fruit flies can enter the Subpod when you are adding your food waste. They can also get into the system before your food scraps are added to the Subpod. This can happen when there is a loose lid and the sneaky little fruit flies sneak in when you are not looking.
Do you have a kitchen caddy/container with a tight sealing lid?
The more thoroughly you stir your food waste into the bedding, the less likely you will have a problem with fruit flies and other insects. If you add a bit more moist bedding (moist carbon), it is easier to bury the food waste thoroughly when you first getting going.
Also, make sure that the larger holes on the sides of your Subpod are below the soil line in your garden bed.
You can leave fruit fly larvae in the Subpod (the tiny cream coloured larvae), and they will slowly diminish over time if the above techniques are used.
If you don’t like fruit flies in your garden, there are some simple non-toxic solutions like this fruit fly trap: https://youtu.be/AnDCReoxdHo