External mic could sort it. If itself does not hit anything, it will not pick up those knocks (at least not that loud). Otherwise you can't avoid recording that, because hitting something generates sound, and microphones only job is to capture sounds.
Once the clicks are already recorded, you will need to either cut them out, or manage to create a very similar sound, and invert it, to try to remove the clicks with that, in a good audio editor. But that one is a lot of work.
If you're riding the Guzzi, you should slap Droid noises over the clicks and knocks.
More seriously, if it isn't during dialogue, then cut the audio out, cut in and out two seconds of audio before the empty space, clone that two seconds and fit it below the empty space and trim accordingly to fit in the empty space in the audio channel on the timeline. If its during dialogue, go with the Droid noises.
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