I wouldn't clean the diode window over something that small, I have larger dots in my best laser but you can only see them when it's unfocused so it doesn't matter, and mine don't rotate with the lens, that means the diode, if it's not broke don't fix it, it's too easy to make it worse, however Bowtie is right, see if they rotate when focusing. I keep a lens cap on my lasers because I live in a dusty environment and it's easy to ruin a lens by burning someting on to it so it can't be cleaned, although this generally applies mostly to more powerful lasers.
Alan