I had the same reaction as you at first, but read carefully:
"Mostafavi and his colleagues tested more than 8 million common mutations, and found two that seemed to become less prevalent with age"
Old people are less likely to have this gene than young people. This can have two possible explanations: old people with this gene are more likely to are already dead (and thus not show up in the study), or the gene is becoming more prevalent in the younger generations. The statement "People without these mutations have a survival edge and are more likely to live longer" favors the first explanation.
This is not the effect of natural selection on gene prevalence. (And it would be weird for Alzheimer's, which usually occurs at an age where reproduction is often finished, and maybe even raising the kids is done already).