Sebastian's comments are important. I'd like to also add that the difference in the derivatives is expected. Simulink's solver solves for states and outputs sequentially from block-to-block while Simscape compiles all the states/equations and solves simultaneously. This is why the Simscape derivative output appears to be able to "look ahead" to have the correct derivative a time-step sooner.
I have attached a model that illustrates this difference. In the "StopFcn" callback, a plot is created of the Simscape Position, Simulink Velocity (i.e., the output of the "Derivative" block), and the Simscape Velocity. I have used a fixed-time step of 0.1 seconds so the values easy to compare. Notice that at time = 0.1 seconds, the output of the Simulink Derivative block is simply (Position(0.1) - Position(0))/0.1. This is due to the sequential nature of Simulink's solver. But the Simscape solver simultaneously solves for the position and velocity using other model equations/states (like force/acceleration). This allows it to pinpoint the correct velocity at 0.1 seconds.
