This just happened to me, and I found the problem. In the MCCC mod there is a setting in the pregnancy section that will allow you pick the number of babies for a pregnancy. I had mine set at 2 ( I accidentally messed this one up, I thought it was the number of babies allowed), and let's just say that my town nearly doubled in population. I have since set the number to 1, and the twin situation stopped.
There are two different setting in this area, one is for the pregnancy itself (single birth, twins, triplets), and the other is the total number of babies a sim is allow to have during their life time. Just wanted to mention this.