There are occasions when a passport is held up because further investigation is required. Sometimes State will reach out to the applicant for individual follow up and sometimes there will be nothing said.

If on the other hand, the delay is because an application slipped off someone's desk, a note from a Congressional office will shake it loose. If the delay is due to further investigation, the response to Congress is usually something vague such as "national security followup."

For what it is worth, this can be as simple as having a name and associated information which is fairly close to a "bad guy".