The truth is you are never going to know. Employers don't tell you because there are liability issues involved and they are always going to cover their backsides first.
But it could be because you lied on your application even if it was a lie by omission, like you forgot to include one of your arrests, or didn't include them believing that only convictions would be checked. Most jobs would only check convictions, but some jobs, especially those that require licensure, look a bit deeper into your criminal background. In the US it is done by requesting your FBI file, which differs from your criminal record. Your FBI file includes every time your name appeared in a Police report. By omitting those facts on your application shows a lack of integrity and motivates suspicion, which is why they may deem you unqualified.