My preferred phrasing is "The only difference between practice and theory is that, in theory, there is no difference between practice and theory."
Indeed. Just take a look at Murphy's laws of combat: http://www.murphys-laws.com/murphy/murphy-war.html
I'm quite sure that if there is one set of people that know this by heart then it is the military. Real world experience will bring out the trouble much faster than any amount of simulation.
Use simulations to help you design, validate your design in the real world. Then update your simulation to reflect the lessons you learned during your real world tests and iterate.
Have a look at armadillo aerospace, John Carmack is as versed as anybody in that field with simulations and STILL they find out almost every trial they do that the real world is not as clean as the simulated one.