You should always refrigerate leftovers within two hours.
Also, break it down into small containers no more than a few inches in depth and make sure they are put in the fridge in a way that allows for air to circulate around each container. Don't stack them, at least not until they are 40 degrees or below. A very large container of soup put into a residential refrigerator is not going to cool quickly enough to prevent dangerous bacterial growth. The outside might get cool quickly, but the inside won't.
If you do these two things, and your refrigerator is cold enough, I'm guessing it should fix the problem.
I'm a bit of a food safety freak.