Plot hole: Clark uses his x-ray vision to see the remains of the girl in the wall, which seems to establish the wall is not made with lead. However, he only reacts to the Kryptonite bracelet inside until he is aware it is there, despite the fact he should have been able to feel its effects long before that.
Plot hole: At the start of the episode Samantha is shown putting the sniper rifle together during the start of the speech. The second time we see this scene, after getting the backstory during the rest of the show, the scene plays out that Samantha is backstage kidnapping Lois at the start of the speech. This would mean that Samantha would have to be in two places at once and she doesn't have any powers at all.
Plot hole: Chloe has to use Lex's thumbprint to access the safe inside level 3. She gets his fingerprints by lifting it off of the flashlight he picked up for her earlier in the caves. The problem is when Lex picked up the flashlight and gave it to Chloe he had only touched the back half of the flashlight, but when Chloe lifts Lex's print she gets it from the opposite end. Since Lex did not touch that end there should be no fingerprints for her to lift and use on the security door.
Plot hole: Clark is delivering presents for Chloe. In the overhead shots looking down on Metropolis he super speeds from building to building and he only spends like one second in each building before going to the next one. This doesn't match what is shown while we see him leave presents by the various trees inside the apartments. In those interior shots he spends 5-10 seconds in each room. The overhead shots are not sped up. Not only do these times not match up but he would also be slowed down to open the doors or he would constantly be breaking them down.