If these were lies, then why had the Rabbi asked her to read them? (4.24)
The Golem, honest and practical to a fault, doesn't understand why the Rabbi would read fiction—and the biblical stories of Noah and the Garden of Eden are tales the Golem dubs fiction.
[The Rabbi] felt obscurely wrong in keeping [the bag] hidden. But then, if a child had landed at Ellis Island carrying a pistol in his pocket, would it not be right to confiscate it? (4.44)
The Rabbi feels guilty that he's keeping the Golem's possessions from her, but he believes he's doing so to protect her. The bag contains instructions on how to destroy her. He doesn't want her destroyed, and he probably doesn't want her knowing how easy it would be to do it.
He had not been honest with his daughter. (5.137)
We're not sure why Abu Yusuf lies to his daughter by telling her that he didn't see the Jinni's palace. Does he want her to just think she's a crazy young girl? Would things have turned out differently for these two if he had been honest, or does his lie not really affect anything at all?
"You must allow me to regret a small lie made in the service of a larger good." (6.27)
Even though the Golem feels guilty for lying to the Rabbi's daughter, the Rabbi believes a little white lie is okay for the greater good. Are you surprised that a man of religion so easily plays with the truth?
Not once during the evening had [the Rabbi] thought of the satchel of books and papers hidden under his bed. (10.105)
The Rabbi has to try extra hard to deceive the Golem because she can sense his thoughts and feelings. This makes the deceit run a lot deeper, because he has to convince himself on the inside to think differently.
Now [Schaalman] could follow [the Golem] without detection, and he need not worry if Levy should bring his new wife around to the Sheltering House unexpectedly. (20.105)
Schaalman has to resort to magic to hide his thoughts from the Golem. Does that make him a weaker man than the Rabbi, who manages to do so without magic? In fact, Schaalman's completely blank thoughts make him stand out even more to the Golem, who can detect the absence of emotion within him.
She'd bound herself to him; she would see through what she'd begun. And perhaps, one day, she would tell him the truth. (21.51)
The Golem's whole marriage to Michael is a deception. We can't even imagine what the truth would sound like. Something to the tune of: "I'm made of clay. I don't really love you. I hate making all these macaroons…"
If you don't bring the money, I will go to the police and tell them the truth. I will say it was Chava who attacked Irving, and tell them where they can find her. (22.102)
We're not sure if Anna is lying here or not, but her blackmail is totally deceitful. She'll resort to anything to be able to support her baby since Irving is a total deadbeat.
[Michael had] woken—or thought he'd woken—to find his wife lifeless beside him, still as marble. But then she was herself again, alive and breathing. Strange, how dream and reality could merge so seamlessly. (22.137)
While Chava might be doing her own fair share of lying to her husband, Michael, by refusing to ask her questions and confront the truth, is deceiving himself.
Is that what you want, for your own mother? To see her soul go howling? […] Looking for her bones that lie rotting in the ground? Looking for you?(23.120)
The Jinni may or may not be lying to Matthew here, but either way he's telling him an altered version of the truth to purposefully scare him away from trying to mess with magic that he doesn't understand.