In Britain, the expression good job when used by a superior to a junior is considered patronizing. It is not used as a compliment.
I wouldn't use it at all except as a joke, if you knew the person you were speaking to would understand the joke.
A simple well done or nice one is much more acceptable and can be used between people of any position.
In the USA, the phrase good job is used much more often and has no negative connotations that I know of.