If you have a car subwoofer and are powering it from a car amplifier, the amplifier can cause the car subwoofer to create popping sounds, so to test if the amplifier is the cause to the popping noise problem, fit a different car subwoofer into the subwoofer enclosure and connect it to the channel terminals on the amp, using speaker wire. Power on your head unit and play a music track of your choice and increase the volume, do you hear a popping noise from that subwoofer?
If you do, then the amplifier is the cause to this problem, if you are powering a subwoofer enclosure that is a ported design, chances are that the subwoofer is bottoming out. When a subwoofer bottoms out, the voice coil slams into the back of the magnet, causing popping sounds to be heard. So make sure that the subsonic filter is turned on your car amplifier, if it currently is turned off, that is the reason why you can hear popping noises. If the car amplifier doesn't have a subsonic filter, then replace the amplifier with a replacement amplifier that has a subsonic filter because it cuts out bass frequencies a human can't hear, which stops popping noises, as the subwoofer no longer will bottom out, if the subsonic filter is used.
If the subsonic filter is on and the other test subwoofer is not making popping noises, then the subwoofer that is making popping noises is blown, as it likely to have a blown voice coil, blown because of overpowering the sub or sound distortion because of the gain is set to high. To find out if the subwoofer voice coil is blown out, press down the subwoofer cone, if the cone is very stiff and barely moves, when pressed down, it proves that the voice coil is knackered, so you will need to replace the subwoofer.