Continuity mistake: When Elizabeth points the gun at Cutler Beckett, a certain amount of her hair is down, but more hair is pulled up in following shots. (00:27:20)

Continuity mistake: When Cutler Beckett enters his office and places the lantern on the desk, the handle is down. However, when Elizabeth walks out of the shadows, the lantern's handle is upright, then down again in a later shot. (00:27:30)

Continuity mistake: Beckett tells Elizabeth that she needs to up her offer. She replies by cocking the gun that is under Beckett's chin. Beckett then walks with the gun under his chin to his desk. However, when he arrives at his desk, the gun is now by his right cheek. (00:28:50)

Continuity mistake: When Pintel, Ragetti and the dog are in the boat, the corner of Pintel's collar is folded up when he says, "Aint that right, poochy?" and also when the dog jumps into the water, yet, it is folded down in the other shots. (00:29:15)

Continuity mistake: When Pintel, Ragetti and the dog are aboard the row boat, extra rowlocks (wooden posts attached to the gunwale) appear behind Pintel when the dog jumps overboard, and then they disappear when the wave flips them over. (00:29:40)
Continuity mistake: When Beckett says, "A marriage interrupted," he writes "Lord" as he signs the Letter of Marque, but when he places his seal, his handwriting differs. (00:29:40)
Other mistake: When the two pirates are rowing toward the beach, and the dog is at the front, one of them is reading the bible. From the cover it's being held the right way up, but in a very quick shot showing the actual text of the book, the text itself is upside down. (00:30:20)
Suggested correction: This isn't a mistake. Pintel states that Ragetti can't read. So the fact that Ragetti has the book upside down adds to this claim. With regard to the cover and text being opposite ways round, Ragetti or someone could have reattached the cover at some point as the Bible is damaged in places.
I feel like arguing that the "cover may have been reattached" is far too much conjecture to be a mistake. It's much more likely to just be a minor continuity gaff as the mistake suggests.
Continuity mistake: When Pintel and Ragetti's boat flips, the boat is seen firmly secure on the beach, well before they end up on the beach. That would only be possible if the waves crashed on the beach with a great force. (00:30:30)

Continuity mistake: When the two women put the necklace around Jack's neck they are stood next to each other and are close enough that they are touching each other as they put the necklace on. When the shot changes they are stood around 1ft away from each other. (00:31:20)
Continuity mistake: When the cannibal women place the necklace of many fingers and toes around Jack's neck, the digits of multi-skin color and size are tied and hang in a specific way. When Jack seasons himself with paprika, the digits are different. (00:32:05)

Continuity mistake: Just before he becomes Shishka-Jack, the rope wound around Jack's arms is higher up at his shoulders, yet it is lower and taut in following shots. (00:33:40)
Continuity mistake: During Jack's escape, as he attempts to flee from the cannibals, when he enters the hut there are silver objects, such as tea pots, etc, on the table, which change position in following shots; and the cup and saucer disappear in the shot facing the table. (00:33:40)
Continuity mistake: When Jack finds the silver spice can inside the hut, the word "paprika" is written in clean white lettering. But once he's outside, confronted by the cannibals, the word is suddenly covered in reddish powder - before he spices himself up. (00:33:50)
Continuity mistake: As Will climbs up the mountain in the bone cage, notice his crisply-white shirt. It's perfectly clean after swimming in the ocean, walking through the jungle, and then being dragged on the ground, dangling by one leg. (00:34:30)
Revealing mistake: When Will, Gibbs, and the other pirates climb up the cliff's 90ยบ rockface, their hair, jewelry, etc do not reflect the gravity which would naturally affect them, despite any wind. (00:34:50)
Continuity mistake: After Jack seasons himself, in the first shot as the cannibals carry him, the rope is wound around his body and ankles, with the excess rope in between that hangs over the pole from his right to his left. When he is placed over the kindling, that rope hangs over from his left to his right. Also seen when Jack tries to blow out the flame. (This has nothing to do with camera angle.) (00:35:30)

Continuity mistake: In the scene where the crew of the Black Pearl is in the two cages climbing up the ravine wall on vines, in one shot, the smaller cage is significantly further behind the one with Will, Gibbs and the others. In the next shot, when there is the conversation about, "it would only take about six," to crew the Pearl, the smaller cage is even with the larger one. (00:35:50)

Continuity mistake: When the cannibal walks across the bridge and sees some prisoners fall to their death and the others escaping, there is a long stick, which has a black design on it, threaded through his lip. When he arrives back at Jack's roasting, the stick's design is very different. (00:36:10)

Continuity mistake: After Jack is hung up over the kindling, to be "roasted and eaten", a cannibal carries a torch across the bridge and shouts. In the cannibal's close-up, the painted black/white sticks pierce his left ear, whereas in the previous and following shots the sticks actually pierce his right ear. The close-up is a flipped shot for continuity of face position. (Mostly visible on widescreen version). (00:37:50)

Continuity mistake: When Will, Gibbs and the rest are in the ball cage and escaping the cannibals, they roll down a hill and hit a tree, which they then roll up. This would be impossible unless the weight is evenly balanced throughout the ball completely. (00:37:50)