I am replacing an old subpanel with a new 125 panel (main breaker in place). The old sub-panel was fed by a 50 amp breaker on the main panel. It appears to only have one hot (the white) and a neutral ground (the bare) coming in. When I try to wire white and black to main breaker, and ground (bare) to ground bar, I only get half the slots. Am I basically getting 120 coming from the 50 amp breaker in the main?

Sounds like the 50 amp circuit is only 120 volts. You should have tested these wires before beginning work, and see how they are connectec at the source.