When Chloe's mascara runs with tears, the marks vary between shots. Most of the time there are no tracks on her left cheek, but one shot has two conspicuous tracks there. The single track on her right cheek varies in shape.
When Jonathon is turning the valve to stop the oil, he turns it left instead of right.
When dawn is looking at Clarks photo in the yearbook, his statement next to the picture mentions hanging out at the lake with PR,CS and "the 2 LL'S . If this is meaning Lana and Lois, Pete was already moved to Wichita by the time Lois appears on the show so, he wouldn't be hanging out at the lake.
As the band is playing right before Clark and Lois enter the prom, the drums are not synced with the music.
Jonathan seems completely recovered from the gunshot wound to the leg that he received from the evil Lex in "Onyx".
Billy is also Troy who drowned in season 2.