The Clinton campaign declined to comment for this article.

Republicans are eager to exploit the issue. House Speaker John A. Boehner has issued a stream of news releases on the emails and the questions he thinks they raise, while the House committee investigating the 2012 attacks on the United States mission in Benghazi, Libya, has expanded its inquiry to include the emails.

There are still unanswered questions: Who at the State Department advised Mrs. Clinton that she could send all her email communications from a private account? What specific criteria did her lawyers use to decide which emails would be deleted on the grounds that they were personal? And what exactly was the classified information that government inspectors say was improperly included in her emails? Outside the political maelstrom, some security experts believe the ultimate judgment of her conduct will come not in a court or from Congress but at the ballot box.

“I think the whole set of circumstances has been scrambled by political considerations surrounding the presidential campaign,” said Steven Aftergood, director of the Project on Government Secrecy at the Federation of American Scientists. He said the inadvertent “spillage” of classified information into an unclassified system is quite common.

“If there’s a penalty,” he said, “it may cost her some votes.”

Others say more than politics is at stake. “I was stunned to see that she didn’t use the State Department system for State Department business, as we were always told we had to do,” said William Johnson, a former Air Force officer who served at the department from 1999 to 2011.

Mr. Johnson said his concerns were only compounded by the discovery of classified information in the emails. “If I’d done that, I’d be out on bond right now,” he said. He said he believed that someone should be punished — if not Mrs. Clinton, then career employees whose job was to safeguard secrets and preserve public records.

“It’s not the end of the world; she didn’t give away the crown jewels,” Mr. Johnson said. “But this is not how things are supposed to be done.”

The email controversy breaks into three clear phases: Mrs. Clinton’s initial choices about how to set up her email; her decision to destroy messages she judged to be personal; and the discovery of classified information in an account where it is not allowed by law.