Welcome to GF! I can't tell what you have without a picture (and even then, probably not). Chances are it's one of the following:
--tiny crickets (do you feed crickets and are some left in the enclosure?)
--grain mites (see this article: How I Got Rid of Grain Mites - Gecko Time - Gecko Time). Theses mites are not anything that will affect your gecko
-- springtails, though if you keep them on paper towels I don't know where they would have come from.
None of those would affect your gecko.