The Home Button on the iPhone SE is a physical button unlike the capacitive one used on the iPhone 7. So the button does make a click when you use it, but some users have experienced a rattling sound or a clicking sound that is not similar to the usual click sound. While some users were able to attribute the rattling to dust and grime which had settled on the button, most users found that it was a problem with the hardware and it required Apple’s attention.
Visit the Apple Store with your device and if it is under warranty then you may get a replacement.