I think it might be a combination of factors that makes this happen, but it seems to be some sort of "noise" that comes from the charging source. With the OG Droid, when it happened, it was quite bad. I couldn't control the phone really at all when it was plugged into a particular outlet in my home office. It didn't matter if I used the provided Moto charger or a third party (or even Blackberry) charger. I could even get the same effect if I plugged it into the USB port of my computer or laptop that were being powered off of the same outlet. If I plugged it into a different outlet (even in the same room), everything was fine.
Here at work, I have found that my D3 (and my OG Droid before it) shows the same condition when charging directly from the wall outlet in my cubicle (using the supplied Moto charging brick and cord), but has no trouble if I charge it through my work computer (which, it is actually plugged into a USB hubbed built into one of the monitors). At my previous cubicle, the OG Droid could charge from either the computer or the wall outlet without any trouble (I didn't have the D3 when I sat there).
The D3 seems much less sensitive to this than my OG Droid did, but it still happens, just not at jittery.
-SR-