The scripting is so broken in this game that playing it in a single segment can often be an rng nightmare with so many softlocks that getting hit by even one can cost a lot of time. I'll try and list all of the ones I've found in this thread so that anyone planning on trying this game can be aware of them.

Pureza:

1. Going too quickly upon first loading the level can cause Taylor not to spawn, breaking the door trigger.
2. One of the most common ones. When skipping the cutscene the game often forgets the mission 3 loadout screen, trapping you in the level. Can be somewhat mitigated by saving before the cutscene starts and reloading.

Bunker: Again, the final cutscene can often forget to bring up the mission 4 loadout screen. Save before opening the door with the keycard.

Seaward Star Interior: It's possible to trap yourself on ladders when coming out of the explosive rooms. Not sure if this can happen on other ladders in the game but it only seems to happen in this level. Best avoided by not jumping into ladders as it messes with your hitbox.

The Armory 1:

1. Entering the elevator before Sam breaks his AI and stops him activating the switch.
2. The final cutscene again forgets the mission 5 loadout screen. Save before entering the room after the "Can't save here" script is deactivated.

Prison: The final door can be unpickable even after killing the boss. Avoided by doing some precise platforming on some crates.

The Armory 2:

1. Jumping on some rubble too soon can cause an invisible wall not to disappear.
2. The level sometimes does not end when taking Sam's body to the trigger point.

The Shop Level Two 2: Running out of ammo in the tutorial breaks the game as the ammo pickups are not actually collectable.

Perimeter: Quicksaving and loading on the same frame that unlocks your save during the parachute sequence will teleport you into the sky and freeze your movement.

Labs 1, 2, 3: Planted explosives sometimes don't detonate.

Lab 4: Mission 8 loadout screen doesn't load after skipping cutscene. This is the worst softlock in the game as it costs roughly 57 seconds to repeat the cargo lift sequence. Saving is disabled before the cutscene. So far the only reliable way of getting past this is to just watch the cutscene.

So far these are the only instances I've found but with the way this game is scripted I'm sure as I keep playing it I'll find even more.