Do you have a lot of thick carpeting plants? Or are they more interspersed larger plants?
I've kept C. pygmaeus multiple times. Each time, the fish have always entered into the "understory" of the tank, and I rarely see them. Presumably, they snack on pods and shrimplets. I'd see them darting around underneath the cover of various plants. In the 10 gallon, they'd hide under the Cryptocoryne undulata (or whatever the Petsmart TC non Crypt wendtii plants were), and in the 29 gallon, they hid under some unidentified stem plant. Each time, there was plenty of open space (Indian Almond Leaves in the 10, a barren field caused by amazon swords in the 29), but they never ventured out from their cover.
So many fish/plants/inverts to keep, not enough aquaria.