Plot hole: Everybody jumps into the water and emerges on the submarine except for Natalie. They're wondering where she is when they notice a flare. They realise it's her, and they send a search party. She's hiding on a bus maybe one to two kilometres away from the water. Her going there makes no plausible sense. Makes no sense how she held her breath underwater longer than anybody that they didn't see her and why she would go in the opposite direction of the sub. It was done to prolong the scene. (01:09:00 - 01:18:00)
Plot hole: Towards the end of the movie, the characters use cell phones to determine whether or not the enemy is coming. However, throughout the whole movie, one of the girls has her cell phone, which never goes off even when the enemy is close.
Suggested correction: When she is on the submarine, the engineer hands it to her and tells her he replaced the broken parts and it works now. That is why it didn't trigger for the aliens.