Outside the secret facility, Mary and Wakeman are stopped, talking on the sidewalk, in a sequence that continues to shift perspective, between the two. Each time we see Mary's face, her hair is pulled forward, completely covering her ears. Each time the perspective shifts to Wakeman with Mary in frame, her hair is pulled back behind her shoulders, fully exposing her ears.
In two external shots of the university, Allie can be seen running up the steps to the door long before she actually arrives there.
Mary says that the UFO project figured out that Charlie was Allie's father "last year." However, in Charlie and Lisa (2002), Dr. Wakeman made this determination on April 6, 1993, nine years earlier.
When Eric asks Dr. Wakeman how long he has been sleeping with Mary, Wakeman replies, "About six years." However, in Charlie and Lisa (2002), they slept together for the first time on June 9, 1993, nine years earlier.
When Charlie meets Allie, he tells her that he taught third grade 'the last three years'. Charlie has been unemployed for a decade.