Welp, time to put my two cents in:
The Company doesn't typically hold prisoners unless explicitly ordered to, either that or they could get into trouble with the local government if they carry out justice themselves. But in the event they are required to hold prisoners, most of the time it is a simple interment camp or a room that's been re-purposed until local authorities can pick them up. In the event they are forced to transport prisoners-they are thrown into a cramped, sound-proofed, air tight, unlit container with an independent oxygen supply-no light, no sound, and an absolutely claustrophobic environment may at times can have an effect on someone, often requiring a soldier to have either a cattle-prod or a dart gun loaded up with enough sedatives that it can knock out a Neko hopped on whatever passes as space crack in the setting.
The rather temporary nature of the internment camps or the unusual means of transport are mainly for logistics reasons-though the containers need to be prepped ahead of time, however it doesn't mean they can't hold people long term if needed. The facilities are just made a little more permanent.
In the event that local governments are unable, uncaring, or just simply out of their jurisdiction and they have the facilities to hold them, the company will administer judgement themselves-chances are if they caught the person in question, they were probably in the process of or had just finished commiting the crime and they had more than ample proof of it. Thieves depending on what they've stolen will receive punishment in two forms; Theft of food, especially out of desperation, would simply see them interned and put to work to understand the meaning of 'Earning your bread', along with learning a useful skill or two so they don't have to steal anymore. Attempts at breaking and entering, stealing a vehicle or mugging would see one's hands broken or put in a stockade and whatever goods that were stolen confiscated, repeat offenses may earn one a similar fate to those stealing food, though likely it being simple heavy labor, along with a brand marking them as thief. More serious crimes, such as murder usually result in being executed-usually via beheading or hanging, though not always.
And since no one's mentioned it yet-in the case of war criminals...the person in question better hope they die in their attempt to capture them they have orders to bring them back in one piece, otherwise it's gonna be a long day there friend.