I have used in my first pregnancy and this pregnancy the Clean & Clear with I think 5% benzoyl peroxide in it. I only use it once a day or every other day not both times I wash my face. If I don't use it, I do break out.
My doctor said that its a category c which means there haven't been enough studies done to show if it could potentially be dangerous. It's best to leave them alone. But talk to your doctor they might prescribe you something if its really bad.