Peppering can be from a few different things.
Depending on the grade of your discus, it can be a natural part of their pattern - though you won't see it in a bare bottom tank, anytime you add a darker substrate or background, the discus will try and match that (usually what's below them, rather than behind them) sort of like what a chameleon does.
Peppering can be a sign of stress, but in my experience (many years of breeding) when a discus is stressed it will show bars and start to turn black.
It's been almost 5 years since I've kept discus, but if memory serves me right pigeon blood's do not stand nearly as much a chance of peppering as solid strains.
Either way, it's pretty much set in stone that most of the discus on the market are going to drastically change in color based around what substrate you have in the tank, and a good amount of them only show their optimal intended color that they've been line bred for in bare bottom tanks.
Doesn't mean it's going to affect their behavior patterns or health, though.