After Having Sex My Boyfriend Noticed He Had Spots On His Penis. Three Days Later I Go To The Doctor And Find Out I Might A Yeast Infection But Now His Symptoms Are Getting Worse And I Had No Symptoms Of A Yeast Infection. Could It Be Chlamydia/yeast?

Your boyfriend is not having yeast infection because this infection is symptomless in males. If your boyfriend is having sores on his genital area then these sores might be herpes caused by either HSV1 or HSV2 . Chlamydia also does not cause sores in males.

Clymidia or yeast infections will show symptoms for the male. They are what they call the carrier. They carry these two things from person to person. They themself don't have the symptoms so they don't realise they are carrying it. To be very safe go to the doctor both of you and get checked out is my opinion. 

My opinion is that it is Herpes. Good luck