I've tried to recreate this with no success. I'll be uploading a run to my youtube to show the run this occured in.

What happened: The game think you already completed Fish, if you complete fish as normal then die to rick then by continuing the game as normal without quitting out of the game. It dose not reset the chapter fish allowing you to skip having to capture the 3 Carp. There could be other triggers that have not been reset it just hasn't been tested much.

If dying, the trigger sets to 1 and remains at 1 until the first chapter is selected. If you quit and rejoin, then select any chapter other than new game, the trigger stays at 1 and only resets when the first chapter is selected. For fish, we need to determine the exact cause of the reset and what prevents it from resetting, and do the same for other triggers to understand how they reset or not.

I never died throughout this playthourgh

granted its like on a save file that has all the files cuz I've speed ran the game multiples times before this

yeah dying is just one of the causes that doesn't reset the fish there could be others too I just know 1 possibly 2.

This is the run that I did where it occured, not sure if there's anything I did prior to the fish skip that caused this to happen.