I dont think the mole had any relevance to a time paradox, but rather, it implied that Kyon was able to see Mikurus breasts close enough and be 'close enough' to her to actually tell her about it. I think that the part about Mikuru not wanting Kyon to get close to her is because Kyon eventually chooses Haruhi over her and she gets her heart broken. (though I would rather be wrong, and have some strange occurence happen instead)