It was a misunderstanding on her part, not a deliberate 'deception' on his (part). [=he didn't try to deceive her or lie to her]
The article describes the government's use of 'deception' [='deceit'] to gain public support for the program.
She 'practiced deception' on her unsuspecting clients. [=she deceived them]
(..) and I found the most talented coder in my company. You know, instead of seeing this as a deception, you should see it as proof. Proof of what? Come on, Caleb. You don't think I know what it's like to be smart? (..)2014 Ex Machina