I have noticed the same rattle/clunk noise in my 90... the same noise the 50-140 makes when it is not on the camera. Both lenses make incredibly sharp images when on the camera and Fuji says the noise is normal behavior. As long as the image quality continues to be so outstanding, I'm not going to worry.
As a long time professional photographer who has used Canon for the better part of the last 25 years and has suffered through numerous QC issues, 1D variant body focus issues, weather sealing issues, lenses that were back/front focused on one side and not the other, repeated IS motor failure issues, just to name a few, I have been very pleased with the high quality of the Fuji bodies (X-T1's) and the glass and how well they work right out of the box.
As far as reviewers "warning" readers about the noise, if it how the lens is supposed to operate and does not compromise image quality, there wouldn't seem to be a need to warn anyone.
I am really loving the 90... clunk and all.