I have been taking the Perfect Pass Probiotic and have noticed occasional dark specks like pepper in the capsule's white power. Is this normal?

Yes, that is totally normal. The strains used in Perfect Pass are 100% natural, direct extracts from fermentation with no fillers added and certainly no colorants added. Fermentation powders tend to have variation in color and even odor sometimes and biology is never pure white. 
When you see pure white powders they are typically mixed with a filler to homogenize color and even bleached or whitened to give a uniform, white colors. 
As you know, there isn't much in nature that is pure white, certainly not anything with bacteria. So those specs are just a natural part of the raw fermentation extract.