My 2 year old had the same thing. First it was Hand, Foot, and Mouth Disease which for the most part it was gone but then some spots didn't disappear. Took her to the doctor this past week and I was told she had a staph infection. Gave her an antibiotic for a few days and now its gone! If it was me, I'd be going back to the doctor. I was always told to push if you feel somethings wrong!