Edward is soaking wet when trapped in the crypt. When Willow rescues him and they climb out, he appears to be completely dry.
After swimming to the Sea Plane, in his boxer short's and t-shirt, Edward swims back to the dock where he is next seen fully dressed and totally dry, except for his hair. Then, while walking up the lane, there is absolutely no water bleeding through to the outer clothing from the soaked undies beneath. Evidence to him having these on underneath is that he is wearing the same boxer's / t-shirt combo after the bee attack when he is dressing after his recovery.
At the beginning of the film, it is made clear that the island has no cell phone coverage, as Malus cannot get a signal anywhere. Yet later on, he receives a call on the same phone.
When Edward and Willow meet near the remnants of the old stone building, he is clearly shown not wearing his sidearm as he stands near an open window; when he and Willow return to her daughter's room he is wearing his sidearm. There were other instances of the on again-off again sidearm, but that is the most obvious.
Officer Malus picks up dirt off of "Rowan's" grave twice.
When Edward slams the beer tankard on top of the bee, we're meant to believe it has been crushed. But when he was drinking out of the tankard, we could clearly see that it has a glass bottom, and like all such tankards it has a substantial lip, which means the bee would have been unharmed.
Though the film ends with a sad ending, as the Summersisle cultists succeed in sacrificing Edward, they wouldn't actually be able to get away with it. Edward had told his fellow officers at the police station that he was going to this island to find his missing daughter, and once they notice that he hasn't returned, the island is the first location they'll go check. Furthermore, Sister Oak killed the Pilot, someone who secures shipments of products and supplies to the island from abroad, and has an employer on land, who will notice if their pilot hasn't returned after his latest delivery.
Edward Malus, a trained police officer, would have definitely noticed if his gun had been emptied of ammunition by Willow before he was swarmed by the cultists. A gun without ammunition feels much more lightweight.
When Edward is drinking the tankard of mead, his face is seen through the glass bottom. A few moments later, he smashes a bee with it. In spun metal tankards of that type, the glass bottom is recessed to protect the glass. He could have trapped the bee, but not smashed it except with the bottom rim, which is too narrow to make such an action plausible.
The shells Willow drops on the ground appear to be .45ACP
rounds, which are significantly larger than the 9mm rounds Edward's Beretta pistol would fire.
There are clear car tracks on all the dirt roads around the island but the people in the movie who live there only walk or cycle.
Obvious CGI bees when they're poured into the helmet cage Edward was forced to wear.
In the beginning when Edward is staring at a truck as it drives by you can clearly see a crew member in the reflection of the truck as it speeds by.
Why did the women kill the pilot? He did what he needed to do, get Malus safe to the island. Furthermore, it is previously stated that they are in secluded private property. Before the twist is revealed, it seems as if the pilot is risking his entire business with Summersisle just for $100.
The residents of Summerisle appear to live an Amish type lifestyle and there are no phones on the island, yet there is a fully functioning website.
When Willow frees Malus from the water the next morning, he is able to walk out and walk normally. Given that he spent the whole night treading water and yelling for help; he should have collapsed from exhaustion, his voice should be hoarse, and has hand should have been like prunes.
Being allergic to bees, you would think that Malus would keep his eyes and mouth closed as opposed to screaming.
Edward finds the Pilot's corpse missing his eyes, hands, and his mouth sewn shut in a gory scene. Though he is quite clearly dead, Edward still tries to wake him up by shaking his corpse.