Just got my desktop this week, and when I was trying to mount the fan, I noticed that the screws won’t go all the way through. If I use the duct, the screw tip will not reach the other side. And even if I remove the duct, the tip will pop, but I don’t have enough thread to screw it in.
Are you sure your fan is completely seated? The studs on the heatsink should go into the holes in the fan, but for some Noctuas they bind and don’t slide in easily (was the case for me as well). There are a few topics about that here where one suggested to use the screws to pull the fan down over the studs (which is what I ended up doing).
Also, the install guide mentions the length of the screws (I want to say 28.5 mm but I could be completely off27.3mm), so you could check that as well.