It's never nice to hear about problems with a new Apple product, but that's the case with the new iPhone SE. The Apple support forums are currently showing a number of reports of distorted sound during phone calls made with the iPhone paired through Bluetooth to a wireless headphone or car audio system.
The problem exists with both iOS 9.3 and iOS 9.3.1, and it's happening everywhere that the phone is being sold. Not every user is having the problem, so it could be associated with Bluetooth chipsets made by a certain vendor. Restoring the device, clearing and then restoring pairing, and other changes do not work to fix the problem.
Apple is aware of the situation and has given it a high priority for resolution.