What is primary cause of shock induced separation (shock stall)?
The simplest answer is that a shock wave for a boundary layer means a sharp adverse pressure gradient. You probably know already that adverse pressure gradient will thicken a boundary layer and thick boundary layers are more prone to separation. Also, if the adverse pressure grad. is so strong, it can immediately produce a detachment of the flow from the wall.



Add to this that a separation bubble forms in the near region and this interacts with the shock. All these phenomena are quite complicated and to explore their underlying physics Large-Eddy Simulations (LES) are used for the Navier-Stokes equations. This is a topic of Ph.D level research. If you want an introduction you can check this source and discover further on your own.