Even though Apple only presented iPhone SE in March users keep getting issues with both iOS 9.3 update and their new 4-inch smartphone [Apple has already fixed iPhone lock screen bypass issue]. The most recent reports mention iPhone SE audio issues. These are not common problems and they are only experienced when you are trying to make a phone call via Bluetooth.
If you are trying to use Bluetooth headset or take a phone call in your vehicle you can come across iPhone SE Bluetooth problems. You might also get issues with GPS voice navigation. At the same time, it seems that the music streaming option works perfectly well and is not affected by the same bug as Bluetooth support.
It also looks like firmare version cannot fix your problem since both iOS 9.3 and iOS 9.3.1 iPhone SE users have the same bug. Since reports come from different countries including the UK, the U.S., Australia and other places – the bug is not a carrier specific problem. It is most likely related to Apple software or other issues.
It is curious that iOS 9.3.2 beta testers also get this issue so this is something Apple will have to fix on its end [compare new iPhone SE vs iPhone 6s]. The number of complaints keeps growing and this should be something the Cupertino-based giant has to consider and address.
You might try to reconnect your Bluetooth equipment or turn on / off Airplane Mode but this wouldn’t solve the bug. Even if you try to change your SIM card you won’t get away from the issue. The good news is Apple is aware of this situation and is working on a fix.