I checked version 0.2, and it seems the error code has been appearing since the power outage in level 3… My English isn't my native language, so I hope you understand.
The main issue is event stacking. There are three main reasons that cause the bug after level 3:
1. Not investigating the puzzle on the left engine, or not investigating the computer in the order you designed. This can even lead to event stacking when the puzzle restarts, or the ending being replaced. This is because the player has already completed the puzzle and then re-enters the repair mission, resulting in stacking.
2. The code stacking occurs when the player completes the repair puzzle and during the second power outage in level 3. This causes the player to run out of stamina to continue solving puzzles, and returning to the crew quarters means they can't interact with food or leave the crew quarters due to the power outage, resulting in a soft lock.
3. Finally, there's the engine puzzle, the one with the infinite 30 seconds, which you've already repaired. However, another puzzle also fails to trigger due to stacking, requiring save/load (SL) to reload the event. There's also a chance that the malfunction won't trigger again, resulting in a soft lock.
My personal suggestion is: Disable the timer or reset it when completing specific repairs. This will simplify the game and definitely eliminate bugs.
Also, the timer should be disabled when completing main story missions. I noticed that the timer wasn't disabled when completing repairs on the third day.