The one issue with the smith machine, as previously stated, is that it locks you into one range of motion. Thus, if a body part hurts in that specific range of motion, there is nothing you can do to alter. The only thing you can probably do is use lighter weight.
However, if youre using free weight, it allows you to use various ROM's and different angles. As such, if you find an angle where the body part doesnt hurt, then you may be able to go heavy.