The System only had 2, and the other one blew up. It's not impossible they had a third, at the very least some of those Liberator style fighter craft they had may have still been knocking about.
Was it mentioned on screen they only had 2? I know they called them deep space vessels (or something similar) but I did not hear any reference on how many there where. Even so, after 2 years presumably they built more.
Speaking of that, was it ever mentioned who was fighting on 'Space Fall' obviously the Liberator was involved and its crew escaped the ship. We know know in 'Redemption' that the were slave uprisings so I wonder if it was a civil war of some type.