Realistically - yes, it can happen.
Here's the reason:
The brake pads will "float" a bit. The floating action will be in all three dimensions (right/left/up/down/forward/back). This prevents the pad from binding and will prevent brake drag from happening, thereby preventing unncessary wear.
(This floating action, with pads that have metallic compound can at times, cause a high-pitched squealing sound. Car manufacturers cannot use pads that contain asbestos due to environmental laws that affect a manufacturer versus and aftermarket supplier. We also do not use soft organic pads since they wear too quickly, and produce massive amounts of brake dust. Some aftermarket suppliers use asbestos pads, they are quieter, but also more dangerous when changing, and wear faster.)
Lazy assemblers will not put enough brake pad squeal prevention backing on the pad, thereby allowing the pad to float up and down to make the click sound. As the rotor turns, the pad (since they *are* new) will also grab the rotor until they break in.
So - you can do the following:
1) Take the pads off yourself and chamfer the leading and trailing edges. Add a boatload of anti-squeal and replace
(I would never recommend adding any anti-squeal compound, these brakes should have anti-squeal shims installed at the suppliers plant where the front corners are assembled. In addition, a "boatload" will cause some to eventually drip onto the rotor and other surfaces. Any use of anti-squeal compound should be minimal, if required. Should I also point out that anti-squeal compound is to be added to the back (metal) surface of the pads, if used. Reason I say this is I had a neighbor once, who put anti-squeal compound on the pads themselves, backed out of the garage, and hit a tree 
)
2) Take it to another dealer - make THEM do step 1.
3) Take it to the same dealer - make THEM do step 1
4) Wait another 500 miles and allow the pads to break in normally.
(I suggest this course for a few hundred more miles.)
5) Make sure the anti-squeal springs are installed. Mistakes are made during assembly.
If you do not see any loss in braking power, you really will be fine. I'm sure F5Fstop will chime in, but there will be some tolerances that are acceptable in new brake pads and new rotors. Yours might just be on the annoying side of the tolerance level...
True. Hard to get good stopping power, low brake dust, and decent wear without using some metallic in brake pads
After 2.5k miles on my wife's H3, all strange noises have either abated or we've tracked them down to their source. It did take that long to get there though..