If you plot the PFD-CP current versus reference-feedback phase difference, the "dead zone" refers to region where the current does not change regarding the phase difference (a flat part in the graph).
This dead zone is due to some circuit non-idealities (switching time and other), which means unless you did model those it will not happen in Matlab.
Simple PLL models (to check stability and loop response) does not take those into account.
You will be able to measure the dead zone from Spice simulation.