I notice the same thing, like little gnats. I don't see them flying around much but notice dead ones in the water dish sometimes.
I think they're more after the food than the soil. I don't see how eco earth can come with gnats since it's compressed and dry (as long as you're getting the bricks). But maybe it has some dormant eggs in it? Not sure but I'd like to know.
With moist substrate, it means you're going to have bugs. They usually aren't harmful.
I'm betting that if you move the food dish you probably will see some very tiny maggots. The tiny gnats lay their eggs in the rotting food around the food dish. If you keep the feeding area cleaned up, grabbing out handsfuls of substrate around that area, you might be able to control it a bit.