As others have indicated, the two spots are the shadows of tiny dust particles. The dust is located approximately 2mm from the silicon surface of the sensor. That puts them on the sensor cover glass inside the camera. Their size will be too small to see with the naked eye. (The distance from the dust to the sensor's surface can be found by using a Dust Donut Distance calculator.)
There is no need to try to remove them. Doing so can just as easily add more or move these around. The use of Flat Frames should remove their effects completely. If you used Flats for the image posted, then there is another problem lurking -- your flats are not properly calibrating the frames as they should. It would seem that your Master Flat frame is under-correcting by some amount.
It is best that you dig into the failure of the Flat Frames to correct for the dust. Can you post a short list of the steps you performed to get to the image you posted? That will help us point you to the reason for the poor flat calibration issue.