Swan. What is the deal with Swan? The pendant she wears and the fact that she's screwing with Vincent's head while he's asleep is proof that she's a Proxy, but which one?
There's a theory on Wikipedia that Swan is a fragment of Monad.
In favour of this theory, Swan clearly has a strong connection to Vincent. To refute that, Proxies in general seem to be very much aware of Vincent - it's like he's a beacon or something - and even capable of forming emotional bonds in an amazingly short amount of time - Kazkis, for instance.
Swan desperately wants Vincent to kill Re-l. Monad is in love with Ergo, and since Ergo is Vincent and Vincent is in love with Re-l, Ergo is in love with Re-l. Monad could perceive this as Re-l stealing Ergo from her, giving her motive to want Re-l dead. However:
Ergo killed Monad proper some time ago and Daedalus never managed to revive her. He did, however, create a clone of her in the image of Re-l, and she apparently had Monad's memories, because she acted on a devotion to Ergo Proxy that Real couldn't possibly have learned from Daedalus. Real/Monad has an extraordinarily childlike personality, perhaps due to her forced growth, which is completely at odds with Swan's personality.
On the other hand, since Real/Monad does have the original Monad's memories, it could be argued that Real and the original Monad have a similar problem to what Swan insists Re-l has in this episode - namely, a split personality. The original Monad could be acting through Real. After all, there's no proof that Real didn't lose time, especially as this takes place inside Vincent's mind in one night.
Swan's reference to the pendant is interesting. "Why won't you just take it off?" she asks. If Swan is Monad, well, Vincent wears Monad's pendant. That line could be interpreted as Monad asking why Vincent won't get rid of her when he loves Re-l.
"I hate men that stink of other women," she says. "And I'm sure she feels the same." Pick one or the other of us? I don't know. She does say, "Take care" when Vincent makes up his mind to shoot himself in order to protect Re-l, which could indicate that Monad was satisfied with him picking Re-l. (Possibly because it ensured that he would protect Real and hence Monad, too?)
This doesn't seem to mesh well with Real/Monad's behaviour in the final few episodes, but if the original Monad is a subconscious part of Real/Monad's mind, this issue being settled to the satisfaction of the original Monad might explain the lack of resentment towards Vincent.
Then again, we don't know if Monad resented Ergo in the first place, despite the whole abandonment and killing thing. I'm not convinced that she was trying to kill Vincent in those first two episodes. I wish we knew for certain whether he transferred his memories to Monad like Kazkis guessed! Ergo wouldn't have had a pendant of his own, so Monad must have given him her pendant - or left it behind when she was taken from Mosk - by the time Ergo cast off his memories. (Come to think of it, guilt over Monad being taken might have been the reason that he needed to forget. Then again, I might just be a sap.)
Honestly, I think you could argue this one until the cows came home. There's no real proof one way or another.
...Goddammit.