What should I do about the brown/ red spots after mixing Epiduo and AHA? (photos)

An appropriate chemical peel may help start the process of treating uneven skin pigmentation.
For uneven skin pigmentation I also recommend a skin regimen prior to to prepare the skin for the peel. 
Melarase AM cream is great to reduce hyperpigmentation and to correct uneven skin pigmentation.
 I also recommend Pigmentation Correction Complex to reduce hyperpigmentation of the skin.
Also avoid sun exposure to prevent inflammation and skin burn injury for at least 4 weeks. Spectrase is highly effective. 
Best
H Karamanoukian MD FACS

You should keep the burned areas moist , Aquaphor can be purchased at your local drug store and doesn't contain and chemicals or fragrances that would irritate the sensitive skin. I would also see a Paramedical Aesthetician or Dermatologist about reducing the chances for hyperpigmentation marks.  They can potentially give you a prescription 4% Hydroquinone cream to minimize any hyperpigmenation from forming and fade any existing pigmentation irregularities. You typically would stop the Epiduo a week before getting a Chemical Peel to prevent this reaction. 
Best of Luck!