If you see "error 53" on you iPhone, Apple did it.
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The error is triggered sometime after a non-Apple tech worked on your iPhone.
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But the problem only comes to light when the latest version of Apple’s iPhone software, iOS 9, is installed. Indeed, the phone may have been working perfectly for weeks or months since a repair or being damaged

The home button has the touchID sensor intergrated. The TouchID sensor is a trusted platform module and has a unique hardware code in it. If the code in the touchID button does not match the code in the chip on the main system board the OS will not authenticate the module and return Error 53. Only Apple has the equipment to re-KEY the hardware keys. Apple introduced this extra authentication step in IOS9 to address some security concerns around impersonating the touchID hardware to get around it as a security module.

To explain why this is important, the TouchID sensor never transmits your fingerprint to the system. It stores a mathematical representation internally. When you "enroll" a fingerprint, you are actually training the sensor to recognise your finger print. When it recognises your fingerprint it transmits an authentication code back to the system board which has the other half of the chipset, that system board chip authenticates the code coming from the touchID and LETS the system know the fingerprint has been successfully recognised and releases the system decryption key for the OS to be able to access user data. If you change either of these chips (the touch ID or the onboard) then authentication is not POSSIBLE. Apple has now decided to lock out the phone in such a case to stop 'impersonation' attacks where the touchID sensor is swapped with a different sensor with different FINGERPRINTS to try and get around system security.

Apple could reverse their recent change, but it would decrease system security, or they could supply the equipment to change keys to unauthorised repairers, but this would also be a decrease in security.