Fungal gnats were the only biological problem I've encountered thus far. Found another bug that I'm still not sure what it is, I'll start a new thread for it. But with the gnats, they are definitely a sign of over-loving (watering) your plants. If you are watering to the point where you have a significant amount of runoff in the pot's saucer, get a turkey baster and suck that H2O up. Some even suggest that you re-use this 'tea' in you next watering, but I suggest finding the sweet spot. Not just the sweet spot, but the sweet time. Forget "scheduling" your watering. Let the plants tell you when they are ready. I'm currently running some 2 gallon fabric pots and I've found that 1/5 - 1/3 gallon every 48-60 hours to be my optimal. Just be sure in the beginning to get a good feel of how your pots are dry and you can use their weight alone to know when to water. You may also notice the leaves starting to droop slightly. This is not a terrible thing, but a very good indication that your next watering should be done soon.
I know this reply is a little late to be much help, but if you ever encounter these little effers in the future, get some sand to cover the top 1/8-/14 of your soil. This is where they come from 99% of the time, (Don't quote me on that!) The sand blocks the young from coming out of the soil and climbing the stalk and becoming adults that can reproduce and wreak real havoc with your grow. (Reproduce in the soil, larvae start eating roots before emerging to become adults and reproduce while eating leaves, getting stuck in buds...) Non-toxic sticky traps are also your friend in this scenario as mentioned above. I tried a few different natural solutions as well, but found the sand to be the easiest and most effective.