The evidence of an affair that forced CIA Director David Petraeus to resign from his position still leaves many unknowns, experts say, including some fundamental questions about the investigation itself.

It remains uncertain why the FBI began investigating the E-mails sent to Jill Kelley, a social liaison volunteer at a Tampa base where Petraeus was stationed as an Army general, and whose connections with Petraeus' alleged mistress and family is not yet clear, according to a Reuters report.

"I'm a little surprised that they would have opened a case on this," says a retired senior FBI employee, with years of experience with these kinds of investigations. "I wonder if there was something else in the original E-mail that raised some kind of concern."

The FBI frequently gets allegations regarding high profile officials, says the source, who asked to remain anonymous due to his affiliation with the FBI. About 90 percent of them are unfounded.

It would require clear evidence of serious harassment for the FBI to begin an investigation for a low-profile person such as Kelley.

"It must have threatened death or something like that," the source tells U.S. News. "I don't understand … what was so heinous to start a federal investigation."

The FBI and Justice Department have not yet explained the connection between Kelley and Paula Broadwell, and specifically what prompted the investigation. The bureau employs behavioral scientists to analyze threatening E-mails to determine if there is any immediate threat, and whether the sender is willing to act upon it.

California Democratic Sen. Dianne Feinstein, the chair of the Senate Select Committee on Intelligence, openly chastised the FBI this weekend, saying the bureau should have alerted members of Congress to the investigation.

The agent and personal friend of Kelley, who initiated the investigation, reportedly told House Majority Leader Eric Cantor, the Republican congressman from Virginia.

For Congress to have been told, the investigation would have almost certainly traveled up the Justice Department chain of command, to at least the assistant U.S. attorney general, if not Attorney General Eric Holder himself. It would have been up to them to decide to inform Congress, says the FBI source.

These officials have declined to comment on when they learned of the investigation.