The studies that found this also found that 1. sperm counts stopped and went back up again 2. men with lower testosterone have more children.
In order to do that, individuals with too low a body temperature would be removed from the group due to infections. This would create a balanced system between body temperature (energy expenditure) and bacterial immunity.
With the development of antibiotics, this changed. The previous bottom of the group is not culled anymore, removing the barrier of the imbalance. Therefore, the group is 'safely' selecting for lower body temperatures.
The theory is that in wealthy countries with good public health, there's less need to maintain a high body temperature to fend off threats. The show said that human body temperature "has been steadily declining for decades at a rate of, like, .05 degrees Fahrenheit per decade." (though not in less developed countries)...average is said to be more like 97.5 degrees.
So it's possible this reduction reflects a change in our diets