I think you're right that it wasn't mixed properly.
Many types of whole wheat bread are actually partially whole wheat flour, partially white flour. That could just be some white flour that didn't get mixed.
Alternatively, it could have been a clump of flour that either didn't get hydrated or didn't get yeast mixed in, so it didn't rise, and thus didn't bake the same.
It could also be some dough conditioners or wheat gluten that didn't mix.
Assuming there isn't some other reason to doubt it (e.g., its old, was stored improperly, tastes or smells weird, etc.) I'd guess it's safe.
Best bet is to call the manufacturer, or just return it and get another...