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It’s hard to say. I suggested milk intolerance as it is one possibility. I suppose eliminating it for a while to see if the acne clears would be one way to test.
I cannot see why taking prebiotics would cause acne. Unless of course it is caused by die off and you are detoxing through the skin. The amounts you are having sound ok, but if you suspect you are not tolerating prebiotics too well, maybe cut down a bit and build up slowly.
Of course the acne could also be caused by hormonal fluctuations.