Psycho Pass is having all these weird plot wholes because it is trying to normalize the storyline and world theme. It isn't incorrect in doing so, but it makes it hard to follow at times as common sense will fail>
What this means is that because of the world that PP is in, following Sibyl and all. The second season is trying to 'normalize' the events so that everyone new there doesn't know/care about the events of others that can't be detected in the past.
The second season is defending these plot holes by relying on the Sibyl system (hence the plot hole of the dominators going missing) and it being just. Sibyl knowing all, and being all powerful and just is pretty much the answer to most of the plot holes as of the current moment.
There is a lot of outrage in other forums and from Borisu about the plot holes. The series knows this, they reference and answer questions to plot holes EVERY episode. Even in the newest one, I've noticed that they go out of their way to add tid bits that answer these questions. However, just because you can try to answer a question, doesn't mean it is right. Most of how they are answering these questions in the series are extremely poor. Just because you realize it is going on and am answering them, doesn't excuse the schitty plot holes in my opinion. PP needs to step its game up a bit more.
HOWEVER, it should be noted that this is a valid formula used in film making. Lots of highly rated films have premises that fall flat to semi-plot holes that the film addresses. The formula/idea here is that the director/storyboard artist wants to make this fantastic story/plot and so will go through any way of getting the series to such a climax moment without a 100% focus on the logistics of getting there. Lots of media do this.
PP is doing it much better than the rabble is, but it is still clearly seen.