Lots of colored dots on long exposures. Is this normal?

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Here is an example. I have already run the image through the dng cleaner app.
 
Not sure exactly what you are referring to. I would say the image is "grainy" but that is a result of pushing the camera sensor to it's highest ISO which is a result of needing to increase the shutter speed to one high enough to avoid blur. Can you pull the camera setting (ISO and shutter speed) to confirm?
 
Not sure exactly what you are referring to.

I think he means these dots ..



Most likely, street lamps and lights that become overexposed by slow shutter speed.
Have not seen the dark in the middle before, but sometime will surely be the first ..
 
Got it - I haven't seen that before either. I wonder if the DNG cleaner thinks those are hot pixels and is trying to correct them. Maybe look at the RAW file and see if they are there and look the same.