Continuity mistake: When Richard and Francoise are making love on the beach. They begin kissing deep under the water and continue all the way to the top. When they reach the surface they can stand up in the water which appears to be waist-level.
Revealing mistake: When they are burying the Swede on the beach, you can see him blink when they throw sand into grave.
Continuity mistake: The photo that Richard downloads at the end is clearly not the one taken earlier. There are people in different positions, and one guy who was standing on the ground when the picture was taken is missing completely.
Factual error: When Richard goes to the mainland with Sal, he calls back home to say that he is OK. International phone calls cannot be made from the blue public phones of the type he uses. Only public phones from CAT (Communication Authority of Thailand) can be used for this purpose. Richard was calling from a TOT (Telephone Organization of Thailand) phone.
Continuity mistake: The size of Richard's fish changes size when he stabs it with the spear. It also goes from having no stripes to stripes.
Continuity mistake: When they first get to the island and they are playing cricket, Keety is telling them all the rules of the game and asks "who doesn't understand?" Richard and Etiene raise their hands - when the angle changes, Richard's other hand is raised.
Revealing mistake: Take a good look at the crowd of backpackers waiting outside the office in which Richard just has been questioned by the police. They are the same people that later in the movie are welcoming Richard to their happy, secret paradise island community.
Continuity mistake: At the end, you see Richard downloading the picture from Francoise. In the first shot of the computer downloading the picture, you see an ad at the top of the computer screen. In the second shot of the computer it's not there. In the third shot of the computer it's back again.
Continuity mistake: Daffy tears the screen between his room and Richard's to talk to him. The tears are different when Richard jumps up to talk back.
Continuity mistake: When Richard and Daffy are smoking a joint in the hotel the length of the roach and the colour of the rolling paper change between shots.
Audio problem: When Richard is in the hotel and Daffy bangs on the wall, he bangs it twice. The first time he bangs it, the wall moves. the second time the wall moves about a second and a half later than the noise.
Continuity mistake: When the four tourists are killed by the farmers the last one to die is the girl with the map in her hand. When she falls the map is in a stream of water and starts to float away. Two shots later the map is secure under her hand.
Other mistake: In the first scene between Richard and Daffy, Daffy calls Richard by name, even though Richard has never told him his name.
Plot hole: After witnessing two friends getting killed by massive shark bites (as well as Richard's shark encounter) they all choose to swim away from the island together; even though Sal and Richard used a boat to get the mainland carrying multiples bags of supplies. The newcomers also arrived with multiple kayaks which Richard was aware of before seeing them all get shot.
Chosen answer: In the alternate beginning, Richard is sitting in front of the large Buddha statue when a taxi driver stops and prompts him to take a ride with him. He explains that they celebrate New Year's by spraying each other with water guns, and gives one to Richard. While riding in the taxi, Richard sprays others and gets sprayed, having a lot of fun. It ends when Richard enters the "mall" where he will eventually meet the guy who offers him to drink the snake blood in the regular movie beginning. In the alternate ending, Sal turns the gun on herself and commits suicide. It ends by having a large ship rescue all of them when they're stranded at sea, banned from the island. The final words by Richard are something to the effect of "I have a lot of scars," which from what I recall is the actual ending of the novel by Alex Garland.