Really, I felt that Aosoi was already ill before she left that room she locked herself in. Looks like it's caught up with her.
I don't think that Bowman had been controlled by those military guys. Bowman was real to start with. It was definitely, Aosoi after she cleaned the original servers that Bowman could no longer be used especially from outside. A simple smartphone with very little power is not capable of processing such advance AI tech yet a simple chat bot, but I am amazed how long the batteries last, I guess there's still plenty of power around somewhere considering the school had to rely on solar panels. Everyone else except Yuki knew about Aosoi controlling Bowman. (After all, how could Bowman have said to use a stretcher if it wasn't working?)
It seems as though Aosoi knows she hasn't got long and also knows that their phones may have been tracked. One thing she can do is slow down these guys and buy time for the girls to escape, but it's unlikely even Aosoi knew they where nearby, maybe just preparing otherwise she would have ward if they were been tracked. It did seem like she was on lookout. The twist could be they could actually be trying to save them, there could be two different groups. One bad the other good. They may not have even known, they were nearby. Just searching.
The question really is, what about the university? What if they return and find it has been taken over? and their other friends have been held hostage in return for Kurumi? Since it was never stated it was Kurumi. Aosoi could say it was her who survived the infection and they wouldn't know. Could it be that she actually has cured herself like kurumi when she was experimenting in that college room. Probably not but she didn't seem in good health back then either.
It seems to be moving at such a slow rate, hope they get it done with soon.