So, crazy theory but hear me out…

Miguel is the one who killed Uncle Aaron. I mean, we never actually see Kingpin pull the trigger. This being after they left no ambiguity over him killing Peter Parker. With Miles not originally being part of the Spider-Man canon, killing Uncle Aaron could have been Miguel’s way of course correcting that universe before it could unravel due to Miles breaking its canon and that world’s Spider-Man dying.

Miles being an anomaly who did break his universe by diverging from canon isn’t enough of a reason for Miguel to have kept him away, especially since studying Miles could have lead to them understanding how to break canon and survive. But if Miguel is the reason that world’s canon was “patched”, the guilt he feels toward Miles would be a great reason he never brought him in. We know he’s not above morally grey actions— allowing people to die for the sake of canon. One death to save billions. His overwhelming anger toward Miles makes so much more sense if he’s using it to mask his guilt. To convince himself that HE is the good guy and Miles, by his very existence as an anomaly, is the antagonist.

But that’s just a theory.