When Lana takes the pistol out of the box, it has no magazine inserted. She proceeds to racking the slide and firing two shots. When she puts the pistol back, a magazine is clearly visible.
When Jodi Keenan and Lex Luthor are down in the tunnels, Lex comments that a cell phone won't work because they are too far underground. Jodi says that her's will and hands him a satellite phone. Those phones require a line of sight to the satellite and wouldn't work inside a building much less underground.
When Lana shoots the locks off the briefcase,she manages to not only put no holes in the case but, doesn't shatter the glass desk it is sitting on.
In the video Lana found in Lex's briefcase, the lady says "welcome to Patagonia" and then they show a waterfall in the background and a zoner attacks. There are no waterfalls that big in Patagonia.
In the past, Clark has been completely demobilized and incapacitated by kryptonite. However, he is somehow able to manage to get through the small opening in the tunnels although the tunnels had kryptonite all over.
During Clark and Lex's conversation in the tunnel, the gate, chain and padlock are all intact. After the cave-in that buries Clark (which from Lex's perspective should have killed him, yet Lex says nothing), the gate is completely bent and deformed, allowing Lex to escape. But the explosion that caused the cave-in appeared to be localized to the area around Clark, quite far from the gate.