Cleaning your face and ridding it of makeup before you workout could help... The pores do dilate when working out because of the sweat so if they are open and getting filled with the bacteria of the makeup, that could be the cause of your breakouts...
Another thought is that your body could be ridding your body of impurities and it is showing up thru acne...
None of the above has any scientific backup
but just my personal experience... Ooops just found
an article that kinda says what I just mentionned... HTH...