Well, none of those are particularly good sources. FM, Pandora, and the dated Bluetooth in that head unit don't offer very good sound quality. Can you try a CD, then at least we can rule out the source material being the issue. Without a subwoofer, the OEM 6.5's can only do so much to reproduce bass. Pushing a 6.5" below about 80hz is asking for issues. I don't know what high pass filter the Dyn setup uses, but I wouldn't be surprised to find that one or more speakers is blown. Testing with music that is known to be good quality will help isolate the problem, so pop in a CD that you know, and listen for the same issues.
Also, clear your door pockets out, a candy wrapper, a pen, or anything else will resonate with it's resonant frequency is played through the speakers. The noise could be from a buzz, or rattle somewhere other than the speaker itself.