The Abbott Nutrition facility in Sturgis, Michigan, which produces much of the U.S. supply of baby formula, shut down in February, bringing production lines to a grinding halt. Following a voluntary recall and investigation by the Food and Drug Administration and the Centers for Disease Control and Prevention, the stoppage stemmed from a bacterial outbreak whose effects would be felt months later. Starting last September, five babies who had consumed the plant’s formula contracted bacterial infections. Two of them died.

The production pause is now contributing to a national shortage of formula, a crisis that experts believe will continue for months. Abbott, however, disputes that there is any link between its formula and the infant illnesses.

Questions are now swirling about alleged problems at the Abbott-owned factory, which produces popular brands such as Similac, Alimentum, and EleCare. A recently disclosed whistleblower document claims that managers at the Sturgis plant falsified reports, released untested infant formula, and concealed crucial safety information from federal inspectors.

But eight years earlier, the formula industry rejected […]