The U.S. Food and Drug Administration report noted numerous instances where consumers complained that different products were packaged together, for instance berry-flavored Pepcid chewable antacid tablets were mixed in with mint-flavored Pepcid tablets.

Shares in J&J, which runs the plant as part of a joint venture with Merck, fell 2.5 percent. Merck slipped 1.3 percent. The facility makes widely used consumer brands, including heartburn drugs Pepcid and Mylanta.

"How do you get mint into berry if you're controlling your manufacturing process?" said Jan Wald, an analyst with Noble Financial Capital Markets who predicted it could be costly for J&J to fix the litany of quality control lapses cited in the new report.

J&J is grappling with quality control lapses at two of its other plants that have forced it to recall tens of millions of bottles of Tylenol and other popular consumer medicines.