If you plan on speedrunning this game, you'll have to keep in mind these can happen during your speedrun, so you'll need extra patience (specially if doing so in a single segment).

These seem to be level-specific, happening when certain conditions are met: they don't seem to be exactly random.

However, I'll try to explain them to the best of my understanding so that they can be avoided during runs (can't guarantee runs being always free of these since I can't reproduce them 100% of the time).

1) Softlocks:

These lock the player and/or leave the player unable to progress, resulting in being unable to do anything besides quitting or restarting the level. These are the ones found so far:

1.1. The Bigger the Boat...(potential): if you die facing the main mast while the armored plates are still on, it's possible to get a character stuck inside. It might be possible to get both characters stuck inside and possibly get a softlock, though characters stuck inside the mast can still act (unsure if getting Jack stuck inside can make burning the mast impossible, specially if there aren't 10 bombs left to use the special's finisher).

How to prevent it: try to avoid facing the mast when low on HP during the level.

1.2. Silver Mine, Cloudy Lining: if you have an enemy or enemies nearby when the first platform's supposed to take you two up, and your AI-controlled partner tries to go towards an enemy and stands at the very edge of the platform, it will result in the cutscene starting but the platform not going up, getting stuck. At times this lasts 5-10 seconds only, but that's not always the case.

How to prevent it: simply use Jack's bombs to prevent enemies from coming close to the platform before you get on it.

1.3. The Damsel and the Dead: If you're firing the cannon to break the last wall in the level there's a chance of a pirate hitting you as you switch characters or try to simply stop using the cannon. If this happens and you see your character goes through the cannon (or notice the cannon being intangible), and the wall didn't break, then you're stuck as it seems there's no other way of getting past the wall, resulting in a softlock.

This may happen in Pirates Cursed and Even Worse too.

How to prevent it: use Jack's special to clear the enemies nearby (keep in mind that, if you use the jump finisher, burnt enemies run amok around the area, possibly standing in the way of the cannon shot).

1.4. Where There's Fire, There's Blacksmoke: After the cannon minigame aboard the ship, both characters can get locked in place with their models being invisible, with only the swords being visible to the player. The characters can still be damaged but the enemies soon stop attacking the characters, effectively forcing the player to start over. It seems impossible to die in this state as the character gets locked and becomes invincible when around 5-10% HP. At times it only happens to 1 character, so it's still possible to complete the level, but the invisible character will remain invisible until the next level (maybe it actually happens to both but the player manages to fix one?).

The cause may be either related to the player's actions prior to boarding Blacksmoke's ship or their actions during the cannon minigame.

How to prevent it: right before getting on the ship, perform a forward roll as you quickly switch characters. This will result in the cannon minigame starting with you taking control of the character that was further away from the ship, and then proceeding normally to the boss fight.

I've managed to play the level about 20 times in a row without it happening by doing this, hopefully it's a 100% fix.

2) Crashes:

These cause the game to freeze, then shut down itself on PC. The exact cause is unknown.

So far I've only found one.

2.1. The Last Shot: if you attack Barbossa when he's holding a shield while he's close to a wall, there's a chance of this happenning. A possible cause may be a different attack being called at the same time Barbossa is in "shield mode", since enemies can get hit by a mysterious invisible force around Barbossa at times (could be the spike attack, the cave-in counter or his "tackle" counter, although it's probably one of the first two). It seems like this crash can happen whether Barbossa has high or low HP, so possible HP thresholds are unknown.

Please let me know if you experience softlock/crash issues so that I can add them to the list to avoid the possibility of them happening during speedruns.

If you do lose a recorded run to a softlock/crash, do let me know via PM and we can talk about Crash%/Softlock% as Misc. categories (so that your effort goes somewhere).

There is another on the Bigger Boat level, it is if you head up the stairs as the 2nd set of conquistadors are about to become enemies, the game will register them as still sitting and you sometimes have to restart the level, but its not always the case as you could switch between the two characters multiple times which sometimes, can fix it.

Edit: I just found out you're referring to the glitch mentioned here:

https://www.speedrun.com/potc_tlojs/guides/00caa

It's called "Invisible enemy glitch", and it seems to be solved by defeating all enemies remaining.