Why and how do atmospheric properties sometimes vary from the ISA?
An ISA standard atmospheric day is really more like a global average.  Locally and regionally, there will always be deviations from the "norm" based on the natural cycles of the sun.  Overnight the temperature will cool, then the sun will rise and things will warm up again.  This phenomenon also produces variations in the pressure and density over larger areas.

Otherwise, what specifically do you not understand about how and why local and regional conditions are not always "standard"?