What color was the desk top before you sanded it off? It's generally never a good idea to sand the finish off wood. It should be chemically stripped and then sanded. Sanding a finish off you run the risk of removing the finish on the surface and leave what has penetrated into the wood. This may not be the reason for the specks, it may have been too much of a jump between 100 grit and 220. The specks may be scratches from the 100 grit which the 220 didn't get. It may also be some of the old finish that didn't get removed. It also helps with the sanding if you would dampen the wood and raise the grain between grit changes. From where you are I would take paint stripper and clean off the stain and then sand it with 150 grit followed by 220 grit and stain it again.