Minor time steps occur if your model has continuous states. It occurs during the integration stage of your model. Simulink uses a numerical integration algorithm such as ODE45 to simulate a system. During the integration stage the solver obtains the derivatives from the system and uses it to compute a new state vector for the next time step. This entire process is called the integration phase or minor time step.
Page 3-16 of the Writing S-functions manual (version 3.0) shows a graphical representation of the calling sequence of an S-function which should help to make this more clear. This is also shown here:
