Top U.S. military leaders who oversaw missile strikes last year against al Qaeda targets in Yemen suspect they were fed misleading intelligence by the country's government and were duped into killing a local political leader whose relationship with the president's family had soured.

On May 25, 2010, a U.S. missile attack killed at least six people including Jabir Shabwani, the 31-year-old deputy governor of Yemen's central Mareb province. The Yemeni government provided intelligence used in the strike but didn't say Mr. Shabwani...