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One possibility is natural bran particles, especially if the flour used is less refined or stone-ground. Another cause can be caramelized milk solids from butter. During baking, butter can brown slightly, creating darker spots that may even enhance flavor. Oxidation is another factor—if the dough has been stored for a long time or thawed and refrozen, slight discoloration can occur. In some cases, residue from baking trays can transfer onto the pastry, which can easily be avoided by using clean pans or lining them with parchment paper.
