Because we are all built differently, we all move differently.
No matter how hard they try, they can never reproduce a natural flowing movement in a machine that is specifically tailored to your body. This is a contributor on why you feel sore using machines.
Machines have a set field of motion and your body will probably not be comfortable moving in that field.
Most people use the machines to learn the proper motion of the exercise and move to free weights to mimic that exercise.
The concensus is that freeweights offer a greater amount of concentration supporting the weights in the flow of the movement, resulting in better muscular development.
Personally, I try to use freeweights for most exercises with the exception of a few that i dont feel comfortable replicating. I have a hard time feeling comfortable replicating flies, so I stick to the machine. Other than that, most is all done with freeweights.
not the most scientific explaination, but just my 2c.