Guinea pigs generally are quite placid little animals and tend to like company especially if they are used to each other and females are less likely to fight than males. Do you know if they were reared together or how long they have been together? Do they have plenty of space? It could be that the bigger one is more agressive and may not take to living with another.
You need to watch the sore spots on the smaller one and bathe them in a saline solution in case they get infected.