I don't think this is food related, so the switch is not a big deal. YARD, what is going on outside during play when your not around. Digging, nesting, thorn bushes, bee sting ect.. ??
Something else, should not be a big deal, they heal up and go away. It does not look like fungus. I have never heard of acne on animals and I don't know it all. Tell them/us activity's. One dog I had - had a bump like that on his front upper gum line. It went away after my friend played with him with a toy and the bump was disturbed, by the toy. Wierd story.. Google: dog mouth sores, it's close enough..