In the scene in the sub, after it starts to fill with water, and Sun is trapped, Jin, Jack and Sawyer are trying to save her. Sawyer gets hit on the head. Each time the camera angle changes, the water level changes with each shot. It starts at chest level, then at the neck line, and then back to chest level. Since Sun is pinned against the wall and can't move, these scenes have to be shot at different times.
In the final scene on the beach, Jack stands up and has sand on the back of both legs. He then walks toward the beach and only has sand on his back. When he reaches the water, the sand is covering his entire right leg and left foot.
When Jack discovers the bomb in the backpack, it says 3:54. The beep sounds as the clock counts down, one beep per second. Counting the beeps would set the timer to 3:40, but after the break commercial, the timer is in 3:45.
In the sub after Kate gets shot, Jack tells Hurley to go find a first aid kit. Moments later, Hurley comes running back in saying he can't find one. Yet all the while in the control room where Lapidus and the captain are there is a first aid kit clearly mounted on the wall behind Lapidus.