A: "<statement>. [<suggestion/imperative to behave accordingly>] Do you understand?" B: "I understand."

I claim that in normal human communication that type of exchange is viewed as B accepting what A says, unless B somehow signals explicit disagreement. Then, if B knows this, and assumes that A thinks likes this, and only explicitly affirms understanding while withholding knowledge of their disagreement, B is at the very least deceiving A.

Of course Moody should know to be more paranoid in what he forbids Harry from doing. Especially with him having witnessed Harry showing cunning and paranoia on a level he finds promising.