Dear Leanardo,
The FAST S-Function will use extrapolated values of the inputs from Simulink when advancing from time step n to n+1 (linear or quadratic extrapolation, depending on your setting of InterpOrder). This extrapolation may cause problems (e.g. the spikes you are seeing) if the pitch-angle command is not a smooth function e.g .when stepping up the pitch angle as you are. I would suggest ramping up the pitch angle with a smooth function to avoid problems with the extrapolation (preferably with a function whose first derivative is defined e.g. an S-shaped curve would be better than a step or a linear ramp between distinct pitch angles).
Best regards,