Uncoordinated flight (roughly, not being turned in the direction you're flying) feels very weird when you're experiencing it for real. It's also an ingredient of a deadly spin if you let other things also get out of control. On a sim, you won't experience much more than a certain dial reading a certain reading, and the plane will more or less fly as expected. It's important to learn coordinated flight "by the seat of your pants" to have the habit of adjusting the rudder ingrained in your muscle memory.

There are other feelings, such as buffeting before a stall, that you'll miss on a sim. But flight training is very explicit about those situations, so you'll learn them when transitioning to a real plane. Avoiding uncoordinated flight is something that pervades your whole flight experience; it might be hard to retrofit it onto a sim-trained student.

There are other habits, but that's the most notable one when I'm comparing the two environments.