I think you've described exactly what's happening. I've had other cars that did that, but not noticed this with my factory Brembo equipped Mustang which still has the OEM pads in it. Sounds to me like the aftermarket pads are slightly undersized. Also check to make sure the various anti-rattle clips and shims are all in place and that the pad contact points in the caliper holder aren't binding.
Having said all that, and if all else seems in order, I don't think the noise is a problem outside the annoyance factor.
2013 GT Premium Brembo
MGW, Blow Fish, AM Hood Struts
Tinted, Borla Touring AB, ProCal Tune
Full Shelby/Kicker Audio Upgrade