Dr. Bailey says at the beginning of her story that she was an intern in 2003. This would have made her a third year when the show started in 2005. She was listed as a fourth year, as she was the chief resident starting in season 4.
The young Ellis Grey portrayed in this episode had brown eyes - whilst the elder Ellis Grey in the other episodes had green eyes...
Callie claims the case she is lecturing on came in during her third year, however Alex was the intern on her case which would have made it her fourth year as she was Chief Resident and finished her residency during his second year.