Apple "recently" started running all new App Store app submissions through a filter that checks their code for the use of private APIs. Private APIs, which have been prohibited in the developer agreement section 3.3.1, restricts the use of private APIs in apps. While the rule was always in place, it was impossible for reviewers to comb through the code of every application. Now, all apps with private APIs will be filtered out by machines.
Apple hasn't stated their reasoning for banning private APIs , but one likely reason is security, as private APIs would allow it to do something Apple wouldn't have control over. Another reason is to maintain consistent quality, as private APIs are far more likely to be unstable and crashy, as well as running the risk of being broken by one of Apple's software updates.
The information came about during a conversation between high-profile developer Craig Hockenberry and Daring Fireball's John Gruber: