In the time that Red Magic was down, directly after her door was opened, I'm assuming Dr. Magata was able to get on to the roof without leaving any trace of her access to the doors and elevators, since the system was temporarily switched over to UNIX. However, we see her come back in with Nishinosono and the others from the roof. How does she get back on the roof without leaving any logs, in order to kill the director?
He was already stabbed by the time Nishinosono and Professor Saikawa greeted the Director and Miki. The Director already has a knife stabbed at his back and he's acting like nothing is happening while talking to Nishinosono. This was shown on the latter episodes of the anime.