In th Gosepl of John, Christ instrusts Judas to leave,and he does. After Judas leaves, He speaks to Peter about his betryal. In Mark, Judas in spoken to before the Institution of the Eucharist, Peter after. So too in Matthew. Taking these three together, it appears to me that Judas left, the Eucharist was instituted and then Christ spoke to Peter about his upcoming betryal. It just seems more fitting.
We are talking about my own personal interpretation of Scripture, but hey, that's completely legit right ;)
LOL! Well, I'm sure others have noticed this, and I wonder how it was resolved. I'm guessing the Angelic Doctor commented on it at some point. ;-)