On our Myth #2: Pairs Must Be From The Same Litter post, Brittney asked:
I recently bought two piggies from the same pet store. They were together at the store, and seemed fine. However, when we brought them home, they started chattering and chasing. They haven't chased in a few days, and I still experience mild chatter every now and then, though it doesn't seem hostile any more. The pet store...had them in the same cage, then after buying them gave me the parting words of "They're going to kill each other" Poor Dexter won't leave his hut if Murdoc is out and if he is trying to eat and Murdoc even sticks his head out, Dexter runs back into the hut. Is he afraid of him? It has only been a few days. No blood was ever drawn and they don't fight, and when there is chasing being done, it is usually Murdoc chasing Dexter. Will they never get along?...
Without being able to watch the guinea pigs in action myself, I'm missing out on some behavioral nuances, especially with the alpha-male-apparent Murdoc. But based on what Brittney described, this is what I think...
Murdoc is obnoxious bordering on bullying, yes. Aggressive, I don't think so (at least not yet). Dexter is shy, reserved, easily intimidated, sensitive to harassment.
It's likely there is a sorting-out of power in the cage. Or else you have one pig who is not necessarily interested in being an alpha male and the other one, instead of simply accepting that as fact, feels the need to assert himself further just to make it clear he's laying claim to alpha male status...just in case his roommate thinks he can change his mind later.
It's not uncommon to see this behavior when pigs have been pulled from a larger colony. It's possible that in the pet store cage, there was an alpha male. Free from that hierarchy, Murdoc is seizing the opportunity to be alpha male in their new digs. Sometimes, the behavior occurs when there's a change in living environment -- new cage, larger cage, new home. It's as if someone is saying, "Our digs may have changed, but the pecking order hasn't." (For other causes, read our post titled "Will My Male Guinea Pigs Ever Bond?")
I would keep an eye on them and make sure the behavior doesn't escalate in frequency, nature, etc. You don't want to keep them together if the less-dominant one (Dexter) is really getting bullied. For now, I would get a hidey house that has two entrances, such as the Tropical Fiddlesticks houses. That way if your alpha male becomes a real nuisance in a hidey house, your shy one has more than one exit. Even better, have two houses so both pigs have a place to which they can retreat.
Your real gauge is the behavior of the less-dominant guinea pig. If he is increasingly reclusive (and, especially, if he is rapidly so) and all but refuses to be out of the safety of the hidey house while the alpha male is out and about, you have a beaten-down and depressed guinea pig and it would be neglectful to continue to house the two pigs together. Depressed guinea pigs don't eat and drink enough or at all. Pigs that don't eat and drink enough get sick. Sick, depressed pigs don't have the will to fight through illness. The picture gets uglier from here.
I wouldn't let the reclusiveness drag out for more than three weeks beyond what you've already witnessed. If it turns out they can't remain roommates, you can make them neighbors. Just upgrade their cage to a 2x4 C&C cage and drop and tie two grids in the middle, creating a 2x2 section for each pig. That way, they'll still be able to see and socialize with each other, no one will get lonely, and...more importantly...no one will get bullied.