sadly...this is quite a normal thing in most "pumpernickel" breads or bagels, there just filled with lots of cocoa powder and molases to make it look dark and make many think its "real" pumpernickel"

If your interested in pumpernickel bagels, try Zingermans. They make them on rare occasions for a month at a time sometimes a weekend and they are damn good especially if you are looking for a rye bagel made with a real rye sour.

They list when they have special bakes on there site at zingermansbakehouse.com

The funny thing is, I actually enjoy Bruegger's. I made some from one of Peter Reinhart's recipes and obviously did something wrong. I may be  getting offers for them from the National Hockey League.

Not a speck of rye is included in the ingredients, but you do get a whopping 23 percent of your daily sodium intake per bagel.

 Ingredients: UNBLEACHED ENRICHED FLOUR (WHEAT FLOUR, MALTED BARLEY FLOUR, NIACIN, REDUCED IRON, THIAMIN MONONITRATE, RIBOFLAVIN), WATER, MALT, WHEAT BRAN, CARAWAY SEEDS, CARAMEL, SALT, BAKERS YEAST

Nor do they appear to use high-gluten flour, which is really a prerequisite for a good New York, chewy bagel. The caramel is added to darken the bread so you think it's pumpernickle and the caraway seeds are added to trick your tastebuds, since most Americans associate the taste of caraway with rye.  It's a pretend pumpernickle bagel.

Bagels Forever of Madison makes the real thing, using high-gluten flour, rye flour, pumpernickle, flour, etc. - but you might not like the real thing.