Even now, he could not fully accept the idea that Frank had been deliberately killed—it was so utterly irrational. It was beyond all reason that Hal, who had performed flawlessly for so long, should suddenly turn assassin.
Here, Bowman first seriously faces the possibility that Hal could have become a murderer. The notion is so foreign to him, because Hal has been programmed to behave in a certain way and he had been functioning properly. Bowman is legitimately shocked to discover that the technology aboard the ship does not fully function, and that Hal's inner workings had not been fully understood, and he could malfunction. Bowman thinks that it is crazy that this computer program should develop a mind of its own and plot to commit actions unthinkable to its creators.