Because although they have identical genes, those genes can be expressed differently. To greatly simplify this idea - two horses may have the same color genes for a chestnut coat, but they will be different shades of red. The clones all have the same genes which determine that they will have a blaze, but the exact shape and size can differ. And yes, for markings there can be some environmental factors as well (in utero).
It's not the same as the shade of color - those genetics are pure genetics (though diet/environment could make them look a bit different at times due to sun exposure or not, sufficient nutrition or not, etc). Liver is liver, that comes from inside.
But the uterine environment is thought strongly to play some role in the shape and general size of white markings. But the clones are still going to have a blaze, of sorts, if the original did, still going to have white legs if the original did. But the size and placement can vary a bit.
Top Gun had 3 white legs - his clone, Cryozootech Top Gun, has 4
But an original with a little star and nothing else isn't going to sprout a clone who has white legs and a big ol' belly splotch
______________________________ The CoTH CYA - please consult w/your veterinarian under any and all circumstances. - ET
I don't think anyone knows what actually leads to the position and extent of white markings on horses. I've read that it has to do with the migration..or lack thereof...of melanocytes (the pigmented skin cells) to the distal part of the limb bud during early development. If they don't make it all the way out there and proliferate, parts of teh body are unpigmented (white). The same probably directs melanocyte migration to the in the head. White patches = lack of melanocytes. Errors in directions to these cells cause white spots. As people who bred horses liked white patches, these coat patterns stayed in the gene pool. They're definitely inherited.
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isn't always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. That's how identical cells can have different levels of gene expression, and how people and horses and dogs with identical DNA can express that DNA differently and have unique physical features.
People used to say that differences in mare markings are due to the mare's womb, becuase two identical twins can have different markings. But twins from the same horse can have different markings and I think our understanding of genetics and epigenetics has evolved greatly since those first articles were published in the 80s and 1990.