Check the Fox News interview of General Kelley, Trump's Director of Homeland Security, and testimony today of General Clapper, former Director of National Intelligence. They both pointed out that simply renewing your security clearance is very different from being vetted for their cabinet posts, and a cabinet position entailing security like National Security Advisor. Both went through a much  more invasive the thorough vetting and both said it it was way more involved than renewing your security clearance. So Trump should have done a much more thorough vetting as standard procedure-- and he did so for General Kelley, but he either dropped the ball with Flynn either accidentally or intentionally.