In Pokemon Y , I have a Lv. 24 female Glaceon and a Lv. 23 male Vaporeon. I put them them in the daycare together but the guy says they don't like each other. Why aren't they breeding?
That just means that they are different species from the same game, but WILL still breed. If he says that "they prefer to play with other Pokemon" then you know they CANT breed. So just leave them in the daycare and they should give you Eevee eggs.
Considering that they are both in the same egg group and are different genders they should breed normally.
If they don't then it's either the game glitching or you may be overlooking something important(like the genders).