In the flashback to 2002, Pratt tells Dr. Lennox few staff are working because they're at Greene's funeral. Chen and Romano are said to be working in the hospital. However, in the episode "On the Beach" (# 8.21), they were both at Greene's funeral.
In the flashback to 1999, Abby is a first year med student. However, when he joined the show in 2000 (in the academic year of 1999-2000), she was a third year.
In the flashback to 2002, Pratt doesn't sport the shaved head look he had at the time.
In the flashback to 1999, when Dr. Lennox is presenting a talk about ATP, the sound effects suggest that he is supposed to be using a slide carousel to present (which would not be inappropriate for the time period). However, the ATP molecule displayed on the projector is animated, something that a slide carousel would not be able to do since it can only project a single frame.