After the sub 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. It starts at chest level, then at the neck line, and then back to chest level.
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 commercial break, the timer is at 3:45.