At the end of Chapter 4, what discrepancies become blatantly obvious to Ethan?

In Chapter Four, we learn that the last known contact from Ethan and Stallings was a phone call in a mountain town, Lowman, an hour from Wayward Pines. From there, at 3:07 p.m. Stallings pulled out in front of a Mack truck at an intersection in Wayward Pines. Adam also reveals that, strangely, there was no trace of Ethan in the car –not even residual or trace DNA. Hassler is determined to find out what happened to Ethan. Theresa remembers how one of the agents Ethan went to find –Kate –is the one he had an affair with.