- Drug use
- Financial crimes
- Close ties to hostile countries (China, Russia, Pakistan, Iran, North-Korea, etc.)
And at least in my country, it's not the intelligence agencies themselves that handle the security clearance, but rather a dedicated agency/authority that processes all the security clearances in the country.
Now, if you've never been arrested / charged / convicted on the two first points - who would know? I'm 100% some candidates would simply lie.