There are several small flies that could be visiting your garden and looking for a place to lay eggs--usually at the base of plants. The eggs hatch and become maggots or grubs and that is when you would see damage. Adult leafminers are black flies about 1/10 inch long. Other culprits include: carrot rust fly, cherry fruit fly, and humpback-like house fly types bring onion maggots and cabbage maggots. You get the picture. You can exclude flies with horticultural fleece over the crops or discourage their egg laying with wood ashes or diatomaceous earth on the soil around the plants. Here is a link that might be useful: HarvestToTable.com

are there little round circles cut out of your leaves? how big are they? the size of a house fly or the size of a gnat? are they attacking plant or fruit?

The Bt is NOT sprayed on plants. This form of the organic based product is used as a soil soak to kill the fungus maggots that the gnats lay on the soil surface. Most plants indoors can become infectd with these and get weakened by the maggots destroying tender roots. Allowing them to exist in dry soil will just make them move closer to the roots which also contain moisture, so its very hard to get rid of them without the help of a product that is 100% safe for any plants of any kind. Another form of Bt is used to kill squash vine borers. Benefical nematodes can be used as well and they do work better for outdoor gardens however. The tiny packets of these microscopic worms, once added to water will go after the fungus maggots, but the do cost a bit more money compaed to the Bt. Another, but much more harsh method would be to remove the soil from the roots and drown the exposed roots to lots of water for a few minutes. Only issue there is the plants can get a severe case of shock and quickly die afterwards. Indoor plants are much more delicate compared to ones growng outdoors. When I see the gnats here, I put out several of the yellow sticky traps and you would be amazed at how many they catch within 24 hours. These yellow sticky traps can last many months indoors. I also used a similar one outsie along with scent lures for cucumber beetles. By summers end, the traps are just loaded with the nasty bugs. also, my apple trees get a similar type of sticky goo applied to red spheres, that look like apples. There is also a scent lure used there as well. I never get worms in my apples and cuke plants rarely ever die out due to downey or powdery mildew infections carried by the cuke beetles feet.

Fungus gnats can be a challenge. The use of the correct bacterium strain can be very helpful. Bacillus thuringiensis israelensis (Bt-I) will kill the larvae when they ingest it. Mosquito dunks can be broken into pieces and dissolved in your watering can for application on watering day. Use Bt-I laced water everytime you water for several intervals.