Plot hole: In the shot where two of the pirates find Jack Sparrow in the prison, you see the moon shine out over Port Royal and the pirate's hand around Jack's neck is skeletal. While this is happening we know that Elizabeth is being led onto the Black Pearl by two pirates. If the pirate in the prison turns skeletal, why don't the pirates with Elizabeth turn skeletal? It's clear that they don't as Elizabeth only discovers the curse later on aboard the Black Pearl.
Suggested correction: This can be explained that on the route from Elizabeth's house to the ship there is a lot of fog, smoke from fires and gunpowder explosions, so the moon doesn't get through. The moon only get through once they are underway again and the fog is cleared. The prison is much further and higher than the town and so the moon does get through (only sometimes) there.
You're very much mistaken. In later scene pirates turn skeletal when marching underwater, at the bottom of the ocean. Moon is easily able to get through water and this smoke isn't thick enough to block the moon.
How does water compare to fog? Of course the moonlight comes through the water, its transparent. Fog isn't transparent. You can go technical and question how much the moonlight is reflected away before the effect wears off, but obviously the effect wears off when there is no direct moonlight hitting them, as is the case with fog and smoke.
Plot hole: Elizabeth goes to drop the medallion over the side of the Pearl. Barbossa and the crew gasp and take a step forward revealing they want/need the medallion thus giving Elizabeth the upper hand in the negotiations. Why not let the medallion drop into the water below the Pearl and simply "take a walk" to get the medallion off the ocean floor? The crew can walk under water as shown later in the film so this shouldn't be an issue. (00:38:15)
Suggested correction: Why not "simply take a walk" to retrieve that medallion? They have spent many years trying to find this bit of precious gold. If it's dropped, the underwater currents will most certainly carry it away, and if they walk underwater their feet will kick up the seabed making it even more difficult to locate. These cursed pirates have finally found their last missing piece, which would once and for all end their miserable curse, so they will not risk it being dropped into the sea.
Suggested correction: They only got startled from the idea, not realizing yet they could reclaim it easily, they are so close after all. Barbossa is not pleading to her, and they were hardly negotiating, Elizabeth was even only demanding they leave, nothing yet about the gold. All the scene does is give the dialogue needed for them to think her name is Turner, so they would keep her onboard and not just the gold. It's not an important part of the plot that they let her think she has the upper hand, if at all.
