This is a complicated story, very competently written, but I found it a bit confusing in places and occasionally inconsistent or illogical.
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The only technical problems were present and past tense jumps, and point of view jumps (as in ch15/16 when the POV suddenly jumps to the ship).
I had difficulty in a few spots determining the difference between Sam the person and Sam the ship, particularly when Sam the ship takes over Sam the person. Sam the ship pronoun she becomes he, and I'm not sure who is acting.
I can't say I believed all of the premises. I didn't see any logical reason for a huge power expenditure for energy walls, since the facility will never be used for anything but a prison, so why is it worth so much power to make them moveable? From the point of view of someone approving/funding Facility Zero, why would anyone want the ability to dump off levels into the black hole? Seems to be a huge waste of funding. And why would there be no provision for communication with the outside? I realize being by a black hole creates special circumstances, but I can't see prisoners being sent to a place where they couldn't call for help if something happened, like a "Typhoid Mary" prisoner was sent to the station and they required special meds or vaccines, or someone stole supplies meant for the facility and they didn't have enough food.
There are little things scattered throughout that don't make sense. Prisoners are punished for not taking care of their health, but one guy has decaying teeth. Waste is recycled into compost and fertilizer, but there are no plants mentioned anywhere- what do they do with it? While there is a lot of futuristic tech, there is also retro stuff like trays in a cafeteria, old-fashioned laundry (power expenditure in recycling water- why not ultrasonics or something?), and brandy and cigars that just seem to clash with it being 300 years in the future.
I thought the Brookes were on the cryostation, but they were on Facility One. In one place someone gets an eight-to-nine inch deep cut- they were cut nearly in half and survived?
The double time line is well documented, but I was still surprised when there was suddenly Facility One up when Facility Zero didn't seem to be nearly full. It may be because of the outside time line, but as a reader I'm not going to sit around doing the math of how many prisoners arrive per day versus the total capacity. I was also surprised when in a late chapter it is suddenly introduced that Facility Zero is all male except for Jessica. I would think Sam would have noticed that within a day or two of arriving. I didn't see the point of chapter 16/17, or for that matter a lot of the angel background- maybe that's the basis for a future story? Some is pertinent to the ending, but I didn't think all the detail was necessary to this story specifically. I did like the combination of mythology and technology and the author did a great job blending the two.
A lot of this is nitpicking, but when I come across something illogical or unbelievable, it takes me out of the story. I try to give the author specifics since that's what helps me improve my writing. I hope this is useful, and sorry it took so long.