When Ben is taking a picture of the shark tooth to send off for analysis, he snaps a photo with his digital camera, and without connecting the camera to his computer the picture magically appears. The photo has no background and, mysteriously, Ben's fingers are not on the tooth.
When Ben submits his request to identify the shark tooth to the bulletin board, he titles the message "Mystery Shark". When Cat finds it, it's titled "Mistery Shark". In the following close-up when she's reading it, it's titled "Mystery Shark" again.
During the scene in which a young couple make-out whilst on a water slide, it can be easily noticed that at numerous points the shadow of the cameraman following the amorous couple can be seen cast on the edges of the slide.
The megalodon tooth featured is actually not megalodon: it is laterally compressed, lacking a scar and fine serrations, and does not have a v-shaped root. The tooth shown appears to be a member of the genus Isurus, the mako, or possibly what most scientists identify as the great white's true ancestor, Cosmopolitodus.
At the start of the movie, a lobster is caught off the coast of Mexico with large claws. Mexican lobsters are "spiny" lobsters which do not have claws. Maine lobsters have claws and are not found in Mexico.
After Ben locks somehow remotely redirects the fired torpedo to the submersible's position, he exits the sub via the main hatch. This would've been physically impossible unless the sub was completely flooded, which it wasn't.
When the megalodon is attacking the yacht and the party goers are jumping off, some make it to a huge inflatable safety raft. Off to the right of the safety raft you can see a visible yellow line stretching out from it used to keep the raft in position so it does not drift away.
The megalodon appears, and in signaling for help Ben shoots a flare into the sky, which catches the attention of Hector flying in the helicopter. In the reaction shot of Hector (shown from outside of the helicopter) there is a reflection of a fence on the side of the helicopter. Ben is signaling for help out in the ocean.
When the mama megalodon eats Esai and the whole boat; you can clearly see as the shark's mouth emerges from the water that its teeth goes through the boat's motor showing that the hole scene is computer animated. Besides the boat is destroyed inside the shark's mouth and the shark has not even closed its mouth; in fact it never closes its mouth.