The following contains spoilers for Sabretooth #4, now on sale from Marvel Comics
When the Mutant nation of Krakoa was formed, readers could see how each law of the island was created and the logic behind it. In fact, even before Krakoa was a more mainstream nation, they had to punish one of their own; Sabretooth. During a mission, he went against orders and killed humans without permission. This broke one of Krakoa's main laws, and he was punished by being held in The Pit, forever in stasis and aware. Since then, Sabretooth has done his best to break free. But as more prisoners entered, it became clear that Sabretooth's incarceration was a sad reflection of justice as a whole.
In Sabretooth #4 (by Victor LaValle, Leonard Kirk, Rain Beredo, and VC's Cory Petit), one of the latest prisoners of The Pit, a Mutant named Third Eye, reflected on his incarceration and the incarceration of his fellow Mutants. Much like Sabretooth, they had simply acted out of line and broke the rules. But what was more curious was that their actions weren't reflective of a malevolent nature, like Sabretooth was. Therefore, he began to see that the utopia the Quiet Council has praised may have more cracks in their justice system than previously realized.
Of the Mutants imprisoned, they had all broken one of the laws. For example, the Mutants Nekra and Oya were imprisoned because they had killed pirates off of Krakoa's waters to protect the island. These pirates had ill intent towards the Mutants, yet the duo was still sentenced as criminals. Third Eye surmised that this was because they weren't ordered to. Since the X-Men have done their own version of assassination missions in the past, it was more so that these young Mutants acted on their own accord rather than because they killed at all.
Perhaps the most tragic, Madison Jeffries had fallen in love with the sentient program, Danger. Unfortunately, when he wanted to build her a suitable home, it was deemed too inorganic, and Krakoa rejected Danger. As a result, so did the Quiet Council, and Madison was sent into The Pit due to misguided love. A similar misdirection also applied to Melter, who wanted to practice his powers and one day be of greater service to Krakoa. But because he had harmed Krakoa in the process, his misguided desire for responsibility more got him a one-way ticket to The Pit.
Third Eye was imprisoned because his ability to see into the future caused many potential Mutant parents to see that their children may not get the attention they'd need after birth. This lowered the Mutant birth rate significantly and went against the law to make more mutants. Because he simply gave a strong opinion, he was imprisoned. Ultimately, these punishments reflected an idea that the laws were only broken because they weren't deemed necessary by someone higher in power. This is similar to prohibition or the legalization of marijuana. When illegal, these offenses could carry strong punishments. But the moment it was legalized, those that were once criminals were now honest workers.
In the end, these particular punishments caused Third Eye to question whether the crime was worth the sentencing. To him, he felt that the real dilemma was that these Mutants dared to push past their station and were punished for it. It's gone from justice to a way to establish a hidden pecking order where only those with more recognition could do the same crime with no consequences. Not only is this morally wrong, but it could one day negatively affect the island, especially with Sabretooth and his new allies spreading the word of how Krakoa's "justice" really works.