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