Last week the tech firm released a preview version of iOS 10.
Its kernel - the central component that controls how software is processed by a device's hardware - was unencrypted.
The move should make it easier for researchers to flag flaws that could otherwise be exploited by hackers.
However, the BBC understands that was not Apple's motivation for making the change.
Even so, experts say it could make it harder for organisations to keep secret techniques they have used to overcome privacy measures on iPhones and iPads.