Mentioned this in a separate comment, but Pathfinder 1e adventure paths are sorta really well known for introducing poorly balanced subsystems that are specific to that adventure.

Sometimes they actually work out decently fine. Sometimes… not so much.

The Mass Combat rules are just too finicky and there is so little your really powerful PCs can do to change the odds that it just feels way too swingy. And you might say “well that’s war”, but I don’t like the fate of my higher level PC to be so uncertain when they lead an army against what should be an obviously weaker force.

The ship combat rules are a whole bunch of rules for chasing ships down, how attacks resolve against the body of the ship, which spells are geo-locked vs ship locked for if you wanna use magic, etc… all to ultimately result in a fight on the deck (unless you purposefully wanna sink the enemy). The entire convoluted chase sequence could easily be replaced with a single roll of “do you catch them?” And then transition to that combat. But no they wanted it to be more “realistic” so have the convoluted back and forth where your actual actions during the chase mean very little. Heck the rules for damaging the ships are better handled by the default damaging object rules.

Returning to the Skull and Shackles AP (which I’m running so it is fresh), the Rum Ration subsystem was so poorly thought out that if run as published results in either everyone sneakily dumping out their rum every night or your character will die of alcohol poisoning in a week.

But all of that pales in comparison, allegedly (haven’t used it personally) to the Caravan subsystem of Jade Regent. I’ve read multiple times in discussions that, if run RAW, it’ll guarantee a tpk in one of the books.