It seems strange that I encountered this issue with my reservation and upon looking at my reservation the story the agent instantaneously made up is that the issue was a result of my ticket being scanned a second time.

For kick's on my next trip I'll book another round trip. If I have the same issue then I am skeptical that it's some other random issue and the agent made up a story just to give me some type of explanation. If I don't, well then I'll call myself too gullible.

Just because the policy is to scan in/out of WAS or NYP does not mean there is not an underlying technology issue that would result in this type of issue with a reservation.