Metal chips is squarely in the long tail of failure modes that you can't really anticipate (but of course really easy to be smug about in hindsight). It is also extremely unlikely the bearings, most likely these are from chassis frames assy not cleaned up properly.
I had some metaldust and it was from bearings, but op said something flakes and then microscopic particles. Particles = bearings, flakes = chassis or even stickers, but anyway just because of transport you dont trow a server into production without testing and inspection.
I am beeing smug about not testing your hardware as you do it with software....shitty testing is shitty testing, counts for software hardware firmware and everything between. Even for your diesel generator ;-)