Okay, at the end of Home when Mary appeared, she walked toward Dean and just said his name. Then she focused on Sam and told him, "I'm sorry."
At the time I originally watched this, I thought she was sorry about not being able to be there for him while he grew up... After watching AHBL, I'm not too sure.
Was the view of the what occurred in the nursery that the YED showed Sam real? Did Mary know something was up when she walked in and saw who/what was there? Was she more deeply involved with what happened to Sam and herself? Was that really why she said she was sorry in the episode Home?
Too many questions and not enough answers yet...