If it's on the filter, it will vary from one filter to the next, and may be absent on a certain filter. Otoh, the specks are much too small to be on a filter. In what order did you take the exposures for the different filters? Can you repeat the results, ie, can you take flats for the various filters? One exposure per filter should do it. Is it on all the green and blue exposures? For instance, could it be tiny water droplets that were sitting on the sensor, but have dried up since? In that case, you wouldn't see it any more. And it would vary in size/intensity for subsequent exposures. So by the time you got to the red filter, it could have been gone. I'm just grasping at straws here.
Does that happen? My wildest guess is that that wouldn't create specks, but a swiping vignetting pattern or gradient.
In any case, I would take flats and see if the problem persists, or if it was a one time event.