I knew it was going to be a great tale from the very beginning, when Macintyre describes how Gordievsky went back to his (temporary) apartment, and found that all the locks had been engaged. He never did that, only locking two of them.
He knew, right then, that someone had been in his apartment.
“The first lock on the front door opened easily, and then the second. But the door would not budge. The third lock on the door, an old-fashioned dead bolt dating back to the construction of the apartment block, had been locked.
But Gordievsky never used the third lock. Indeed, he had never had the key. That must mean that someone with a skeleton key had been inside, and on leaving had mistakenly triple-locked the door. That someone must have been the KGB.
"The fears of the previous week crystallized in a freezing rush, with the chilling, paralyzing recognition that his apartment had been entered, searched, and probably bugged. He was under suspicion. Someone had betrayed him. The KGB was watching him. The spy was being spied upon by his fellow spies.”