Having one save is annoying. My progress got wiped out when I wanted to go through the training course again. Despite making a named save I had no way of loading it.

Medbay
Loose scrap in the ceiling, never found a way to get it

Tunnels
Level 2 - hard to get the camera to pan to the left side where a secret area is blocked by crates

Process Control
Flesh wall at middle right of map blocks the Ice Ammo Blueprint station. Accessible with Grenade Launcher. Though there is no way to craft this ammo.

Process Control
From Breaker Room 1 go to elevator
Level 4 - Go left
Use Door Control
Level 3 - Head to Breaker Room 2
Get killed by Heavy Crusher
Repeat but this time Door Control will say power down and won't work

The objective that involves locating 3 Breaker Rooms was displayed as 0/3 #objective_group1

Breaker Room 1
Door to Breaker Room 2 is labeled pre_terran_portal_door

Aft Armoury
Shoot large crate on left side with Grenade Launcher to enter the "repairs" area. You walk off the map because this area isn't displayed.

Aft Armoury
In the top hallway the light switch doesn't work right, it seems to have 4 states instead of 2.

Aft Armoury
Take elevator to level 3
Climb down 2 ladders
There's an air vent here with a Baby Crawler in it that is blocked by crates. You can climb through it while still closed.

Aft Armoury
Floor vent switch in lower level doesn't work right (4 states)
What do these vents go to?

Engineering Bay 2
Area above stairs doesn't appear on map

Engineering Bay 2
Top hallway light switches don't work right (4 states)
2nd one has a visible square that lowers each time the switch is used

Engineering Bay 2
Map station doesn't add anything to the map

Engineering Bay 2
Mystery door control panel at bottom says not available

Engineering Bay 2
Room with Big Cousin and Stalker doesn't appear on map when entered from the right side

An objective that involves manually shutting down the purge systems was displayed as 0/6 #objective_group2

Process Station
Elevator air duct doesn't appear on map

Process Station
Door from short hallway is one-way

Rotten Core
Switch labeled pre_terran_switch_small

Never found blueprints for 2 of the mods.

Had a problem where a Baby Crawler fell down a ladder shaft and got stuck briefly. When it reached the bottom it was impervious to bullets. Possibly it got pushed into the background as sometimes happens with falling crates.

At one point elevator call buttons had stopped working. At another point I had lost the ability to jump or climb ladders. Both were fixed with exiting to menu and continuing.