UKC

Recently purchased a new rope from Mammut, the sheath has a small area with some fluffed up threads and some black marks.

Is this a normal imperfection in the manufacturing process or should I ask for a replacement?

I'd guess it's shop soiled.

unlikely to be fatal, your rope will look worse after one use at a sports-crag. 

I had a similar experience with a Tendon rope. In my case it was tiny hard bits on the sheath along a length of about 20cm in the middle of the rope. I contacted the retailer who asked for photos which they sent to the manufacturer. My money was immediately returned.