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.
When Edward first meets Sister Willow in the woods on the island, he makes a motion to close his sports coat. In the next shot of him, his sports coat is completely buttoned. In the ensuing shot of him after a quick shot to Sister Willow, Edward's coat is completely unbuttoned and open again.
When Officer Edward Malus pursues the station wagon, he has his emergency lights on the motorcycle flashing. But, when he pulls the bike behind the pulled over station wagon (a distant camera shot) the lights are not on. However, when the scene goes to a close up of Edward dismounting the bike, all emergency light are flashing again.
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.
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.
The goof items below may give away important plot points.
When Edward is attempting to rescue Rowan, he is wearing the bear suit. He first unveils a mesh cover below the bears nose to reveal himself to Willow then replaces the mesh to protect his identity. At the point where he goes to rescue Rowan, he is clearly seen wearing make up instead of the mesh. Then, after removing the bear suit... there is no make up.
The women reveal at the end that they brought Malus to the island because he has a blood link to the island. But every other man on the island does, as well, because they are only there for manual labor and breeding. Furthermore, they say that Willow picked him out years ago and because of this, he was destined to come to the island to be sacrificed. This makes no sense because Willow and Malus met AT LEAST five years earlier (given Rowan's probable age range of 5-7), and they didn't need a sacrifice at that time because their honey production was just fine. It was only the year before this movie takes place that the honey production was in trouble.