The problem is presented by in the denouement. How did anyone know of the existence of LC and who knew it well enough to know it was broken and so how to fix it? Only one character would have known by default. Lasciel's Shadow. Mab would have known how to get in but how could she know that it was there and broken?
Add Lea and Mab to the shortlist.
Because the Way from the lab leads directly to Lea's Murder Garden, Lea (and Lea-proxy Mab, during Lea's "sidhecicle incident" (and very-likely Mab all the time, invoking the whole
Mab's Handmaiden vassalage)) can open a Way into the lab any time Harry isn't there, and peek in. If Bob is there, they either need to silence him, or hide; but either/both seem possible...
But between Bob getting sent out riding Mister, getting "free passes" from Harry, and Harry taking Bob in a backpack, there's PLENTY of occasions for Lea and/or Mab to gain
complete access to Harry's lab.
This exact thing -- Bob & Harry both being out of the lab -- happens in Proven Guilty; between Harry's attempt to use it, and Bob discovering the repair, & realizing the (prior) flawed state.
Mab could cross Harry's Threshold, leave 99% of her power behind, and
still have more power (and of course skill!) than Harry, for the purposes of fixing LC.
... Bob says something strange.If he recognized it was wrong after the fact why didn't he recognize it before? ...
The error was subtle enough that he didn't
realize it was an error: Bob isn't an infallible expert. Bob had said, "none of the evil geniuses" he had worked with could have created LC; so it was sophisticated stuff, both subtle and powerful. Bob simply overlooked the flaw, it was a "plausible" -- but erroneous -- design.
What WAS obvious to Bob was the CHANGE. Bob noticed that immediately. And he compared the new to the old... and THEN saw what was wrong with the old.