They do mention this in the article:

> As part of the study, the authors investigated the possibility that the decrease could simply reflect improvements in thermometer technology; thermometers used today are far more accurate than those used two centuries ago. “In the 19thcentury, thermometry was just beginning,” Parsonnet said.

> To assess whether temperatures truly decreased, the researchers checked for body temperature trends within each dataset; for each historical group, they expected that measurements would be taken with similar thermometers. Within the veterans dataset, they observed a similar decrease for each decade, consistent with observations made using the combined data.