Weatherby is killed because he has been asking too many questions about Davy Jones' heart and has apparently discovered his secret. However, a major plot point in the film is that the soldiers aren't being told what would happen to them if they stabbed the heart (so they would not hesitate to do it in case they are ordered to); therefore, Weatherby could have only discovered the truth throught Beckett, Mercer or Davy Jones himself, meaning there was no possible way Weatherby asking questions could have led to any major issues for the East India Trading Company. Not to mention Weatherby is only allied to Beckett to protect Elizabeth, so there's no real reason why he would be interesed in the heart or in betraying Beckett, as even if he discovered the secret it would hardly amount to anything in the bigger picture. This is a bit of an enforced ass pull as the scene where Beckett and Mercer are discussing this was a last minute addition to replace a much larger sequence where Weatherby goes on a Roaring Rampage of Revenge trying to stab the heart after learning about the sinking of the Black Pearl and Elizabeth's possible demise, which gives Beckett a more justified reason to think he has outlived his usefulness.
The very film opens with a retroactive Ass Pull that only avoids being a Big-Lipped Alligator Moment because it makes the Spanish Empire enter the picture. In the scene, a strange old man, the Castaway, is found on the shore of Cádiz and brought to King Ferdinand VI, who finds out he is a former crewman of Juan Ponce de León who has remained alive for 200 years thanks to the Fountain of Youth. This man also carries the ship's log with all the vital info about the Fountain, which makes the King interested enough in the item to send an expedition. Now, absolutely nothing about this guy fits within the film's plot: it's not revealed how or why he ended up in mainland Spain after two whole centuries,note The junior novelization causes a Voodoo Shark by stating the guy had been lost at sea for forty years, begging the question as to why he was not found by any random ship back in all that time or just how he got the mermaid tears needed to make the Fountain extend his life. Nothing in Whitecap Bay suggests anybody has been living there for centuries, to the point the Challices of Cartagena are found by the Spaniard right there where Ponce de León left them, and it's quickly established the tears only can be obtained by very improbable means. If anything, the whole character feels like a quick Handwave to justify the presence of the Spaniards without any further background, instead leaving him as a walking enigma.
The same can also be said of the implied curse that animates Ponce de Leon's corpse whenever someone tries to take the map of San Miguel. Even assuming charitably that this is somehow related to the Fountain of Youth, no source of info in the film mentions any curse (maybe the Castaway's log did, but the viewer never gets to hear it, so it's a moot point), and absolutely nothing is explained further.
The existence of Blackbeard's character and powers feels this way when framed within the events of the previous film, where pirate lords from all around the world were gathered in a council in 1729, eleven years after Blackbeard's fake death, yet nobody was aware of the survival of an absolutely legendary pirate whose presence would have been definitely needed in the war against the East India Trading Company - and to top it all off, the same film featured the presence of a particular character, Captain Edward Teague, who was implied to be the Pirateverse's version of Blackbeard himself (and who also has a brief appearance in this film, for extra weirdness). That this installment showcases Captain Edward Teach as a completely different character, who also possesses magical weapons that rival Tía Dalma's powers and whose origin is never explained, comes off as completely jarring. Blackbeard's absence in At World's End can at least be hand waved by Jack calling him "The Pirate All Pirates Fear," implying that he's a rogue agent that no member of the Brethren Court likes or trusts.
Syrena bringing Jack the Chalices of Cartagena at the end is not supported by any particular Character Development, and feels sudden and jarring. She didn't have any meaningful interaction with Jack, nor Jack with Philip, yet now she is willing not only to help him, but specifically to help him knowingly save the life of either Blackbeard or Angélica, the ringleaders of the crew who had captured, manipulated and tortured Syrena and Philip since the start, and who had massacred many of her kin in the process. Her reluctant expression and line imply she is being forced by some bout of Honor Before Reason, but if that's the case, it's never properly explained or even hinted to the viewer.
The film shows Will Turner having started to turn into a fish-man like Davy Jones, with mutated features resembling sealife, but this makes no sense within the rules established in the first film about Jones' backstory. Back then, it was explicitly said that Jones had only turned into a monster when he forsook his duties out of anger towards Calypso having betrayed their deal. However, this doesn't apply in this case - bitter as he might have become towards his task, Will has not given up on it,note He does forsake his duty briefly to save his son from drowning himself, but this happens after Will has already mutated, so it cannot be the cause - and in the same talk both of them refer to the deal as a curse in past terms. yet he suffers the same physical fate as if he were. This is never explained, and as the curse itself is broken by the end of the film, it soon abandons all importance.
For that matter, the fact that the Dutchman's captain is now considered cursed by default seems inexplicable, as the third film had established that it was a deal, a two-part accord, that only made one of its parties cursed because he specifically broke it on the interpretation that the other party had broken it first (a point that works either way, in any case). It's made even more poignant in extra materials, which explicitly claim that Jones' duty was a reward Calypso gave him for his love. Again, in order to charitably assume the gift would turn into a curse under those circumstances, it would have to be established that Will had broken the deal just like Jones did or that he somehow inherited Jones' bad karma, which is never even suggested in the movie.
It is now revealed Jack's magical compass has the additional ability to realize its owner's worst fear if they ever "betray" it. That such a formidable and dangerous trait had never been mentioned or foreshadowed in the four previous films, especially given that the compass changes hands multiple times onscreen, is both strange and jarring.
Also revealed is the fact Salazar and his crew can be freed as Jack's worst fear whenever Jack willingly gives up the compass. This, however, seems to be a major continuity error, as Jack and other people had given it up multiple times in the previous films without apparent consequence. The context and intention behind giving it away is presumably the devil in the details here, but as this is not clarified in the film's explanation, the viewers are left dumbfounded by how the sudden new rule doesn't seem to really make sense.
Minor, but still. Multiple scenes in the film, prior to the climax where all curses are broken, show Jack the Monkey under the moonlight, yet he doesn't turn into a skeleton, nor is his undead state ever mentioned again. Assuming this is not a spectacular goof on the producers' part, it implies that either the curse of the Aztec gold somehow wore off or they managed to find some alternative way to revert it (as the Isla de Muerta was destroyed and thus the curse cannot be broken in its intended way), but the film is silent on the matter.
Henry suddenly having knowledge of who Sparrow's crew members are and, more surprisingly, having a stash of silver pieces to bribe them into helping him. Considering he had reached the island floating on driftwood and had just escaped from prison, the question of where and how he got these feels like it would merit an explanation.
The second film had established Jack got his magical compass from Tía Dalma, which made sense given that her powers would be the likely explanation for the creation of said item. Now, suddenly, it turns out he actually received it later from the hands of Captain Morgan of the Wicked Wench, without any explanation of how this can coexist with the previous plot point.
Salazar and his crew are aware that the Trident can safely free them from the Triangle, instead of vanishing or being erased from existence as they'd more likely believe. However, that they knew this is pretty inexplicable, as they had just discovered the existence of the Trident of Poseidon from Barbossa, and the trident itself had never been used to break the Triangle's curse because otherwise the curse wouldn't have been in the Triangle to ensnare them in the first place. The explanation might be that the insane Salazar cares little about his own safety during his rampage of revenge and only made an assumption to calm down his crew, but he certainly acts as if he knew it with certainty, despite looking slightky skeptical of the Trident back when he found out about its existence.
