'tis the season. We have them by the HUNDREDS. Since my reds are out enjoying the sun today I'm heating the heck out of their tanks to try to dry it out and kill them off. I can't wait until we move and can provide a better balanced bioactive substrate.
If they are fungus gnats then you can get yellow sticky stakes to catch the adults. Won't kill the eggs or larvae but will eventually stop the cycle. Place the stakes where your tort won't get to it. I have them in plants in in my enclosures and that's where I place mine. If they are springtails good luck. Just change out the substrate. Yeah there will be some that say they are beneficial to the substrate, which they are, however they mass produce in large numbers and are super hardy!
There are several species of harmless "substrate flies". They come from the surrounding environment and they are harmless. Out enclosures provided an ideal place for them to live and breed.
I ignore them.
If you don't like them and wish to get rid of them, you'll need to boil, bake, freeze or replace your substrate about twice a month.