FedSmith.com pointed to an article at the Washington Post about bogus background investigations. This is not something you can lay at any particular President's feet, so focus on the facts OK? The bottom line is that some clearances didn't get approved, some did, and some number of investigators were not doing their job and finally wound up in court over it. Can we say with a certainty that we know who might have gotten cleared and shouldn't have and vice versa? No.
Speaking for myself, I applied three times for the Senior Executive Service development program at IRS and got shot down each time in the interview phase. However, I know that on the last attempt the background investigation needed to be completed, and favorable, in order to get the interview. One of the questions asked of my boss: was I possibly involved in any relationships, marriage, etc., that I was hiding from people? They were really stretching for information in my opinion. I guess the fact that I wasn't walking around with a significant other in tow (regardless of gender) made them concerned. Maybe they thought I was an alien from space.
If you'd like a redacted version of decisions made over time at the Department of Defense, take a look here.