Not to be too contrarian to the thread, but I do think this situation is largely a symptom of Euro5, and only requires a bit of wrist recalibration to overcome. It doesn't sound like anything at all is wrong with your bike.
My Interceptor is also a Euro 5 and does exactly as you describe. The first week I had it, I also stalled it frequently. As mentioned by several on this thread, at a light, even when warmed up, a quick blip of the throttle will cause a dip to below idle speed, before the revs climb back up. When the bike is cold, or if you are simultaneously letting the clutch out, this causes a sputter or stall.
I'm quite certain the cause is the ECU having to quickly switch from idle circuit to its low-speed circuit, and back again. Because the idle circuit is particularly lean for Euro 5, the bike coughs for a minute as the mixture suddenly goes from lean to rich to lean. The issue is compounded by the fact that these engines are not particularly torquey/don't have much fly-wheel affect and need a decent bit of revs to get going, leading to stalling if you're not giving it enough juice because the ECU's low speed and idle circuits are too lean to keep the motor going without throttle input.
In fairness, all of my other fuel-injected bikes (early-mid 2000's era) have also coughed on quick throttle blips from idle, so I'm not too unhappy. And from what journos have been saying about the new generation of Euro 5 bikes, rough low speed fueling is pretty common, so the RE 650s could be a lot worse. My fix has just been smooth and consistent roll-ons from idle, and a bit of extra clutch feathering in traffic, and the stalls have pretty much gone away.