After Nathan tells Peyton his secret, she tells him her secret, that she can't whistle. However in an episode of Season 2 (Near Wild Heaven) Peyton whistles at Haley to get her to sit up.
Lucas is at the cemetery visiting Keith's grave. It is clear the date of death is Jan 23, 2006. Lucas then visits Jimmy's grave and his date of death is March 1, 2006. Since Jimmy is the one who "shoots Keith" and then shoots himself, Keith and Jimmy would have died on the same day during the school shooting.
When Brooke admits her fear of not being enough to Chase in the Tutor Center there is a Flyer on a cabinet that reads "Color Guard 2006 Fall Auditions PRIDE OF ARIZONA", which wouldn't make sense in a high school over 2000 miles away from the university of Arizona. (17:05)
When Haley is talking to Skills she lies down on a table and the pillow that makes her look pregnant is visible.
When Skills and Haley are on the roof completing a class assignment, Haley is laying on a table and lifts her arms up over her head and reveals the tan fake baby bump and spandex she is wearing.