Obviously I must have misread the episode or something...

Everyone is talking incest.
To me it seemed there was a twist, I'll explain. Pilcher to me seemed like he wanted Abigail's baby and ONLY Abigail's baby, guessing gene structure or who the child's parents were(Abigail and whomever the baby's father was All American lacrosse player.) The whole point was getting that child. Later in the episode it shows Pilcher changing out Abigail's picture for Kerry, so I see that as both mother and child were going to be placed into the program. Pilcher received a phone call and it was implied that Abi had a miscarriage, but what if the call wasn't that at all? What if Abigail had the child prematurely? Wayward Pines loves it's twists. What if the call was her opting out of giving up her baby, the baby that Pilcher wanted/needed for Wayward Pines? Enter seedy looking hospital and lawyer(?) talking about needing to get it done right then. This, timeline wise happens right after talking to CJ. CJ and David mentioning they are ahead of schedule by about 10 days (meaning that round of cryo-residents deadline was set for the first part of September 2013). This falls in line with what David said to the headmistress(or whoever was at Walcott Prep) at Abigail's school, needed to be done by December. He finds a child born sometime before then (August 27, 2013) and plans on "adopting" the child or finding new parents for it (again this being right after Abigail has the child and no longer wanted to be part of the program). Okay long explanation short answer. Pilcher used Kerry's baby to switch out with Abigail's baby and put him into the cryogenic pod, again he wanted that baby, it was the bridge, it was perfect. He met Kerry she impressed him and decided to change out the basic information (to pass the boards approval) and substitutes Kerry in place of Abigail. Abigail's baby is Jason, Kerry baby is long dead. Jason and Kerry relationship was not incestous. Lastly Jason freaked out, tried to kill his partner and died for nothing. Seems very much like a Wayward Pines kind of twist.