mp4 is a delivery format ..not particularly suited for editing.
It is highly compressed and audio will be a shortcoming due to the way it is stored within the container.
Correct me if I am wrong anyone.
"Popping," or "clicks" can be introduced, when editing Audio, by Cutting at a non-Zero Crossing. See this article for more info: http://forums.adobe.com/thread/770665
Now, that is just one possibility, but I would check that out, to either cure the issue, or get that out of the way early.
You can also add short audio transitions to smooth things out.
I've run into this with several different source file formats while working in premiere and if there is consistent background noise. sometimes there is no zero point to cut the audio at as the above article recommends. The way I've overcome it, as J. Simon said, is by applying a default transition and changing the fade time to something unnoticeable like 00:00:00:02. This is totally getting rid of all pops I have.
Also, please update to 9.0.2.