There are issues with funding those background checks and paying for people to review them. In Oregon, the county where I live that office is way understaffed. Our Republican Congress and the NRA have rejected requests to adequately fund these checks. I don't know it that's the reason why this nutjob got his hands on those guns. Here is an article that covers this problem.
http://www.usatoday.com/story/news/nation/2016/01/19/fbi-guns-background-checks/78752774/
Depending on the volume of gun sales, at any one time the queue of pending cases — which by law must be resolved within three business days — generally ranges in the several thousand. Recently, those numbers have ballooned as high as 13,000. If the cases, some of which depend on local law enforcement agencies finding paper records to satisfy an examiner's search, cannot be resolved within the three-day period, gun dealers are generally free to complete the sales.
"Some (cases) aren't being looked at until the third day,'' Morris said, referring to the increasing volume and limited staffing.
Roof serves as cautionary tale
The enormous stakes are not always apparent, until the first reports of a new mass shooting echo across social media or cable television.
No one recent case underscores the sobering nature of the work here more, officials said, more than an April transaction in South Carolina, reviewed by a veteran examiner at the West Virginia facility.
In that case, which could not be resolved within the three-day period, Dylann Roof was mistakenly allowed to walk away with the .45-caliber handgun allegedly used two months later to kill nine people during an evening Bible study session at the iconic Emanuel AME Church in downtown Charleston.
So, I'd guess that the killer managed to skirt regulations that would have prevented him from legally acquiring the rifle due to clerical error or lack of time to process the killer's application. The system is understaffed. But that costs money. Congress hasn't really been very amenable to supporting the regulation of fire arms lately. But this is just my guess. This will get attention and reported on from a credible source soon.
Edit: And after funding increases are requested the debate will be whether the extra funding is worthwhile because 2nd Amendment. And the cycle will continue.