From the beginning, one of the main threats in Born Not Made has been government “spooks.” In the book, most people don’t believe in magic, and people with magic live in secret from the government. If found, the government kidnaps them and studies them. At least, that was the original premise. Now, I’m second-guessing myself on that.
It started when I realized a flaw in that part of the worldbuilding. The main character, Trace, used to belong to a section of the military that is 100% made up of magical creatures or people with magic. And as I was plotting last time, it hit me that a government military group like that did not fit well with a government that kidnaps and studies all magical people.
What, do they let some of the magic people go if they serve in the military? How could they trust people they kidnapped to destroy what they want destroyed? Or protect what they want to protect?
And who keeps them from rebelling and taking over? What would keep all magic people from rebelling? Especially people who had been kidnapped and tortured? Or had family taken? At that point, people 1. fight back, 2. leave, or 3. hide if they don’t think they can manage 1 or 2 (generally some of each by different members of the group).
Are you hearing what I’m hearing? Yep. That’s the car of the plot running into a few huge, gaping holes. The kind that destroy tires or even swallow cars whole.
It’s solvable. I’m not sure what the exact solution will be, but I see several different potential paths that I could take.
And I’m not going to use the obvious bandaid. The whole “One arm of the government doesn’t know what the other arm is doing” trope or the “super secret part of the government that even the rest of the government doesn’t know about” version of it.
But I only have 2 months left (a little less – Aaaaaah!), so I better fix this and fix it fast. Wish me good luck!
Savannah Knightly 
I’ve never quite understood the difference between mansplaining and giving advice, also you didn’t ask for advice so I apologize on all counts.
One way to play it is instead of the left hand not knowing what the right hand is doing having them be in competition. There’s all sorts of contradictory groups in the government, and even ones that seem like they should work together often don’t. I just read a non-fiction book about how the CIA and the NSA fight each other all the time. One cabal or branch of group in the government sets up the find and dissect plan while another tries to find the magic people before the first group for recruitment. If magic is a secret it’s not like they can have Senate hearing when one group interferes with another. When you’re doing extralegal stuff anyway there could be be various factions with different goals.
Or it could be made to look like that but it’s a scam. The “spooks” don’t really exist except as a way to scare the magic people into working with the magic agency. Maybe they do grab someone every now and then to make it look legit, but really it’s all the same people. Maybe at first they did try and coerce magic people into compliance and when that didn’t work because it did make people try and fight back and then then came up with the specter of an even worse group looking for them so they could come in and play the “good cop”.
One way to think about it is in this world magic is a crime essentially. So think about real world criminals. How do they fight back or rebel? They don’t because what can they do against the power of the state? Once they’re in the system there’s nothing much than can do except go along with the program.
Also maybe it isn’t a plot hole at all. Depending on the focus of your story maybe it doesn’t matter exactly why they’re being hunted. The motivation of the shadowy government forces doesn’t necessarily have to be spelled out for the story to be good. If you’re a game of thrones fan I think Littlefinger and Varys are both good examples. Their motives were not clear at all for the majority of the story, but it was still interesting.
Good luck , and sorry again
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Lol. That’s a lot of ideas! I have the kernel of one I think I’ll explore first, but who knows? I may decide it doesn’t quite fit and switch to one of these or another we haven’t even considered yet. That’s actually my favorite aspect of plotting – how there’s usually far more options than we like to think there are.
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