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That may be from 'signal clipping'. And it may be a fault in the amplifier rather than in the subwoofer.
But the first question about the amplifier and the subwoofer is, What is the output impedance of the amplifier that drives the subwoofer?
And the next question, What is the impedance of the subwoofer?
Also, what is the output wattage (or, Peak Watts, Max Watts, or Maximum Wattage) of the amplifier?
Does it sound normal aside from the clicking?
Do any of the other speakers click, at any time?
Does the clicking diminish or disappear when the volume is turned down? if so, that is likely to be either a failure in the amplifier's peak wattage, inadequate peak wattage to drive the speaker, or perhaps simply a fault in the amplifier's low-frequency response.
Tell me the maker and model of the amplifier, so that I may advise you further. But likely you will end up needing to have the amplifier serviced, by the sound of it.