Here is a test shot at 800 ISO, f/2.8, 1/200, where the slave in Group A was set to TTL at 0 FEC, while the popup flash was set to "--":
You can see that the shadows are not totally black. The shadows are being illuminated by the popup flash.
Here is the same shot, but this time I used the SG-3IR infrared panel to block the popup flash:
This time you can see that the shadows are black. Note also the difference in exposure on the mannequin head itself.
The popup flash's contribution is less noticeable when you use lower ISOs and/or narrower apertures. Here is another pair of test shots, at 400 ISO, f/2.8.
Here is yet another pair, another stop darker exposure at 400 ISO, f/4 (the TTL compensates so the flash exposure is the same).
The popup flash's contribution is much less noticeable but is there nonetheless. Here is the same exposure (ISO 400, f/4) but with the slave flashes intentionally disabled.
With some subjects that have specular (shiny, mirror-like) surfaces, the popup flash's contribution is even more noticeable, as you can see from the gym bag beside the mannequin head.
As shown above, one solution is to use an SG-3IR infrared panel or similar 3rd party product to block the popup flash. Another trick is to use high speed sync. With Nikon, the popup commander can command the slave flashes above the sync speed but the popup flash will not contribute to the exposure. The downside is that you will lose at least 2 stops of power.
Note: for Canon shooters, the Aokatec panel is designed to be compatible with your hotshoe.
SG-3IR Infrared Panel Review
Cheap Wireless TTL? Aokatec AK-TTL Review
ND Filter vs. High Speed Sync