I returned the first Fuji XF 90mm lens I ordered because it had dust inside right out of the box. The replacement was clean but look what has happened after 3 months: specks of dust all over – I counted around 20. I am aware this does not affect image quality but for a weather resistant (WR) lens, I find it hard to accept. Never had such problems with my Canon L lenses (that I have used extensively in all conditions for 10 years) or my other WR XF lenses (35mm and 16mm). I’ll pay the Fuji Service center a visit tomorrow and ask for a replacement, let’s see what they say… My guess is that dust settles in during the manufacturing process and starts spreading after use.
Edit: a friend of mine is having similar problems with his Panasonic Lenses. Apprently, it could be dried glue that starts peeling off from within. So indeed it’s an issue with the manufacturing process, not dust getting in.
Edit: back from the Fuji Service Center in Tokyo Midtown. They took the lens back, it should be fixed within two weeks. Also got the sensor of my X-T2 cleaned. Both for free.