As has been mentioned before, Negative Habit Transfer is something to be avoided. Learning to do things in a certain manner because that is the way the sim works, will cause confusion in the real machine when you put in your control movement and the aircraft does less or more or nothing at all.
A sim will behave the way it is programmed to do, and it is NOT exactly the way a real machine behaves. And unless the cockpit has a 360-degree visual ability, you will be missing a lot of very important visual cues and sensations from a real machine - sunlight through an overhead window, sounds of wind. Screaming instructor.
Sims are hugely helpful to learn systems operation and for instrument flying, but the real thing is needed for the real flying.