Are they guppies or Mollies? Mollies are actually a Marine Species and can be easily acclimated to saltwater, even breeding in saltwater. Guppies, on the other hand, are a freshwater species and won't live long, in full saltwater.
As for keeping fish in a fuge, not at all recommended. I can see doing it, if you have a trouble fish, or a fish in need of healing, or protection from other fish, SHORT TERM. Long term, this won't be a very healthy environment, as the fuge area would typically be too small. Also, one of the primary purposes of a refugium, is to provide a safe (refuge) place for pods to reproduce, without the fear of predation, from fish. Placing a fish in a refugium, defeats this purpose. Now, if you were to keep Mollies, in your fuge, it wouldn't be quite as bad, as they're more of a herbivore, so would much on your Macro Algae, as apposed to feeding on your pod population. However, they're still opportunistic feeders and will eat some pods.