I would guess that it is the phenolic compounds getting oxidised that turns it brown. As seeds change their chemical composition as they mature, it could well be that the immature seeds are higher in these phenolics than the mature seed or else the cells surrounding the seed are more fragile therefore they release these phenolics more easily, I am not sure.
Did the pods get damaged in any way that could expose the insides to the air or did they just brown once cut?