It was revealed by Lady Toni Bevell that the Mary Winchester the Winchester brothers have been interacting with is a fake, reprogrammed version and the real Mary is imprisoned somewhere within her mind where the walls are "impenetrable".
Dean has mentioned the time Mary had a deal with Azazel, when Sam was possessed by Lucifer, when he was tortured in Hell and lost his soul (Season 6) to Mary as an attempt to free her.
Some of the main antagonists of this season have been killed in this episode.
All of the enemies in this episode were human. Aside from mentions of Garth, Devla and Lucifer, no supernatural creature appeared in this episode at all, a rare occurrence on Supernatural even when the enemy is human.
When the American hunters confront Doctor Hess, she addresses Sam as "Dean", indicating that she never met and therefore didn't know the brothers. While this was probably done to further show Sam's change into a strong, independent hunter, with everyone expecting his brother to be the leader, as he always was.
This doesn't make sense however. Even if Hess never knew the looks of an enemy of such a high priority, she can be seen standing in front of all the targets' information - including looks and names - in this same episode.
The best explanation for the mix up despite that, is that in her panicked state she simply didn't have time to, or think to, look at the monitors.