Can a microfiber towel scratch car paint?

Yes, but usually because the towel is dirty, contaminated, excessively rough or used with too much pressure on an insufficiently lubricated surface. Clean, high-quality microfiber reduces risk, but no towel is scratch-proof when grit is trapped between the towel and the paint. Keep towels used on paint separate from those used on wheels and engine bays, and discard any towel that has been dropped on the ground.