How in the hell could a delayed turn into a denied? Your record is clean or it isn't.
On thought, errors.
The FBI database receives contributions from the states criminal justice systems. Entry errors, pending dispositions, or old court information that is not properly updated ... and, you may not necessarily know about it until you perform a background check, et al. Expungement is an example where dispositions in the FBI database may not receive automatic updates. I suspect in some instances these get flagged and it ends up being adjudicated by an agent even if you're factually/fictionally clear in your state.
There are ways to peek into that information, sort-of like a personal FOIA, but it's been a while since I've done that. Typically after a negative response with a time frame in which you can dig deeper into the reasoning.
There have also been reports of misidentification due to biometric similarities between two individuals or erroneous cross-referencing, as well.