If we all came from two people originally, why isn’t everyone’s DNA the exact same?

Although scientists have long recognized that, despite physical differences, all human populations are genetically the same, a study by Stanford University in 2013 concluded that populations from different parts of the world share even more genetic similarities than previously assumed. All humans are 99.9 per cent identical and, of that tiny 0.1 per cent difference, 94 per cent of the variation is among individuals from the same populations and only six per cent between individuals from different populations. Nonetheless, the team found that tiny differences in DNA can provide enough information to identify the geographic ancestry of individual men and women.
Where do those differences come from? One theory is that DNA sequences could be modified during a cell’s development. Yale University scientists have noted that 30 per cent of skin cells in a study group have copy number variations (CNV), which are segments of DNA that are duplicated or deleted. They theorize that such differences could also be found in cells in the blood, brain and other parts of the human body. Keep in mind, though, that they are still talking about .1 per cent of the entire DNA of human beings.