Jonathan Kent: Are you okay?
Clark Kent: Can I answer that in about five years?
Jonathan Kent: Yeah.
Clark Kent: Dad I'm glad you and mom are the ones that found me.
Jonathan Kent: We didn't find you, Clark, you found us.
The Smallville Torch that Lex views on the internet has two articles that refer to past episodes. Pete wrote an article about his trip in a limo called Take Yourself Out Of The Driver's Seat ("Hourglass") and Chloe reprinted The Most Controversial Speech Ever Given In Smallville by Lana's mother ("X-Ray"). See more...
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Continuity: After Lois and Clark find out that Cooper dies, and after Lois leaves, while Clark and Geoff talk about how Lois is trouble Geoff hair keeps going from neat to slightly messed up. When the camera is behind Clark, Geoff's hair is all shaggy on the left side of his face. When the camera is behind Geoff, his hair is fixed so that the loose strands are tucked behind his left ear. These changes repeat throughout the scene.
Factual error: Clark finds Lois in the sewer and decides to use his heat vision to destroy the lock of the gate that is separating them. Clark uses his heat vision on the lock and the lock explodes, this is a very minor explosion. It also causes the door to fly off the hinges. Now the explosion from the lock is odd since heat vision causes things to melt and not explode, but Clark wasn't even using the heat vision on the hinges and they are destroyed. This is inconsistent with how his heat vision has been shown to work before.
Continuity: After Krypto comes around the fence we hear one of the two guys say "You got all the bags out of the truck, right?". The camera then pans over to the van and you can see, under the rear of the van, two gas containers. There is a metal one on the left and a plastic one on the right. Krypto starts to run for the truck and we see the containers again only now the metal one is on the right and the plastic one is on the left.
Continuity: Clark goes to see Lex about the dog. Lex, who was about to start a game of pool, breaks a fresh rack. Lex then goes to make his second shot from near the side pocket and as he does you can see there are two striped balls near the rail close to Lex's cue stick. Just after he takes his shot those balls are gone even though those balls had not been hit.
Plot hole: In episode 4-16: "Lucy," there is no reason for the criminals to be chasing Lucy on the ski slopes at the beginning of the episode. We learn later that she's been working with them all along; she calls Lois during the chase, and the call is part of Lucy's plan with the criminals. Lucy being chased by the criminals would make sense given the story she gives Clark during the next part of the episode, but it doesn't make sense for what we ultimately learn is the truth. And nobody from Smallville is anywhere near the ski chase, so it also doesn't make sense as any kind of a ruse.