I've never encountered this clicking with any of my tortoises, so I can't really discuss that with you, but members on here talk about it all the time...usually with the redfooted tortoises. Is the clicking coming from his beak?
I've encountered this many times in many baby margies. I think it has something to do with the way their beaks grow. Regardless, I've never known it to be a problem. Margies make all sorts of noises. I think it's funny. My largest Big Gino makes loud breathing noises due to an irregularity in his nasal cavity. It's always funny given that I can always find him by following the heavy breathing sounds.
My Marginated, Samson, is always clicking at us. Not sure if they do it to get attention or not, ours clicks when you put food down, put him in a bath or sometimes when you set him down to walk around on the ground or back in his enclosure, other times he just does it for no apparent reason. Funny thing is that he sometimes scares himself and quickly puts his head in after making the click sound! I think its normal as long as there are no other signs of illness.