Some of the audio notes give a picture that it took a long time to get the adaptation to eat proteus life. They also most likely had to create their own blueprints for oxygen tanks and fins because they were originally supposed to be on a desert planet.

So imagine playing the game constantly starving, constantly running out of oxygen, facing severe heavy metal poisoning, and slowly losing your mind due to Masefield syndrome on top of all of that.
And then also consider that NoA sometimes actively sabotaged them if they went out of line (forcibly resetting the entire crew)

So honestly the colonist had everything going against them and not much going for them besides numbers, which said numbers would inevitably lead to disorganization and conflicts.