I had the exact same pinprick problem on my brand new Paperwhite except my two dots were on the lower half of the screen. Very small but still noticable. I asked for a replacement and I should have it within 4 days. This isn't uncommon. It actually happened on my Nexus 7 as well (busted pixel, not pinprick) and I got a replacement for that too.
Long story short: Amazon has great customer service.
This happens a lot on the Nook GlowLight too, except much worse. Check it out.