I had ugly clicking noises coming from the headset before and after a warranty exchange of a fork (the reason for the exchange was on the other end). I have identified the clicking as coming from the interface of the top cap and the stem. I tried screwing the top cap more and less before tightening the stem but it did not help.
Then, after long searching, I found out at some forum that it could be the loose expander plug. Indeed, when I opened the top cap the bolt below was completely loose. Tightening it very slightly removed the ugly noise. As you can see in the picture the the sides of the stem are still touching at the upper pinch bolt.
Now the question if it is the compressor bolt (no. 6 in the manual) that should be tightened to 6-9 Nm according to https://shop.fullspeedahead.com/en/files/index/download/id/90c31726193366031700722438038db1319/ , how is it possible that it was completely loose? Is it prone to get undone or was it an assembly mistake? Could it damage the carbon steerer when the stem is tightened on an uncompressed steerer? Is it safe for me now to just tighten the bolt, install the cap and mount the stem? I am not sure I trust the bike shop with this anymore, although it is a large company that publishes their own maintenance videos.
Another point is that the referenced manual recommends a 2 mm spacer above the stem. There is no such spacer in my setup, nor there is one in other pictures of bikes of the same manufacturer. There is a 4 mm spacer below the stem. Should I move it above the stem? Is it connected with the fact that the there is no gap now at the upper pinch bolt?
A secondary issue: The photograph of a higher end model shows a rubber dust cover over the top cap. I do not remember having such a piece on my bike, I only remember the cap was very loose once soon after the purchase. Is it important for keeping the dust out of the headset? Under which name can it be bought? If it cannot, I would just put a tape over the opening.