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A few weeks ago I made a Caciotta.   It has not had much mold growth overall but I have noticed that is has yellow spots on it.  What could these be? (The black spots are cracked black pepper not molds)

Sometimes blue mold can leave stains like that.  If you've washed the rind previously, then that's my guess.  They do not look that bad to me.  If it grows and covers your whole cheese with flourescent yellow, then it's an infection in your milk, but otherwise it's fine.