One other thing I want to point out: the investigation is being handled by the police, not the PRT. The PRT handles the parahuman side of things, yes, but as far as the police know, this was just a regular crime that resulted in a trigger event, as opposed to a crime committed by a cape. If the evidence points to Sophia, and they look up her name and find it flagged with a redirection to the PRT, then things get interesting, but they're still the ones responsible for handling all aspects of the case (including getting and executing the warrant for her arrest), so the PRT would then have to restrain her and surrender anything and everything that amounts to evidence. Given the PRT's prior level of cooperation, as much as they might not want the negative PR, it's more-or-less out of their hands at that point, so the best they can do is cooperate fully and completely so that they don't appear to be obstructing justice (which carries penalties of its own).
More than likely, the PRT would remain responsible for keeping Sophia in custody (no, I'm not really spoiling things here, because this is entirely within the hypothetical realm at this point), but the evidence isn't parahuman and so isn't their problem. See, if the evidence isn't properly handled, then any defense attorney worth his weight in beans would have it declared inadmissible as evidence, since it could've been tampered with, if the chain of custody appears to have been broken. If the only direct evidence they have of a systemic bullying campaign against Taylor are the contents of Sophia and Emma's cellphones? Dragon hacking them would fuck that right up (and yes, this is something I admit I fucked up bigtime in AA v1.0).
As pertains to the fic as it is now, no, I'm not considering a third rewrite, that would just be silly. Yes, characters make mistakes (that is, if they're not Mary Sues), and an absence of hypercompetence is not evidence of an idiot plot.