If the spots only occured on the thrid coat, then you can probably sand
the last coat off. As long as you don't sand through all the poly
layers, you won't affect the stain.
Did you do anything to the surface in between the 2nd and 3rd poly
coats? How big were these spots? are they all in one area, or evenly
spread out? How many spots do you have? Are they close together?