Invisalign seems to have exacerbated my gum disease, what should I do?

I have just finished three months Invisalign treatment to close a gap in my from teeth. I did have some active gum problems before I started the treatment, but my dentist seemed to think it was OK to go ahead with the treatment. I had two bouts of Gum Infection during the treatment, for which I was prescribed antibiotics. I continued the treatment, but have now stopped wearing my nightime retainers because my gums are getting irritated and becoming sore. What should I do ?