Drug history. The FBI's current policy allows candidates to apply after one year of abstinence from marijuana, while use of harder drugs generally requires ten years of abstinence to be eligible. Follow-up questions usually aim to confirm dates and details, not to catch someone in a lie about whether they ever used anything at all.
Gaps or inconsistencies on the application. Your Standard Form 86 (SF-86), the national security questionnaire submitted through e-QIP/e-App, is compared line by line against what comes up during the personnel security interview. A mismatched date, an unlisted past employer, or an omitted detail is far more likely to trigger clarifying questions than the underlying event itself.
Financial history. Undisclosed debt, unresolved judgments, or patterns that suggest financial vulnerability can prompt more questions, since financial pressure is a documented factor in insider-threat cases.
Foreign contacts and travel. Given the national security stakes of the role, unreported foreign relationships or unexplained travel patterns commonly generate clarifying questions.
Prior conduct that wasn't disclosed upfront. This is the single biggest driver of extended interviews, and it's worth its own section.