I'm curious as to why sometimes atmospheric properties don't match the ISA's. One reason I am considering is due to calibration discrepancies. By atmospheric properties I mean temperature, Density, Pressure etc.
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"?
The primary reason for the non-ISA conditions is, as Michael Hall stated in his answer, the sun.
Local differences were also explained by Michael, I'd like to add the main contributor to global deviations from ISA: the shape of the earth. As we move further away from the equator, the radiation of the sun hits a surface that is more and more slanted in relation to the direction of the rays, and therefore the energy is divided over a larger area.
Because of this, it is impossible to have equal temperature globally: near the poles its always colder than on the equator. And this opens a whole new can of worms: weather is born. Great differences in temperature over latitudes induces up- and downdrafts, transferring energy(heat), moisture etc. over great distances and creating areas of low and high pressure. Add earths rotation, and it gets really complicated really quick.
This Wikipedia article will give you a brief(ish) description of this phenomenon.
For brevity,I'm not going to go into the effects of the tilted axis of rotation...
In a sense, if atmospheric conditions were always ISA, the weather would always be the same. I'm not wise enough to say what that weather would be...
The reason we need ISA is that have inherent global differences in atmospheric conditions, and that we have changing weather (well, they are very much connected, but best name them both). If we would not have defined ISA conditions, we'd have no reference point, and no way to globally calibrate certain instruments.