How tall is your stallion? How tall are your mares?
Usually, "if there's a will, there's a way", and short stallions will successfully cover taller mares, but there are always exceptions. Are you pasture breeding or hand breeding? How old and experienced is the stallion?
Having seen the result of a mini stallion breeding a TB mare I'm going to guess that's not really an issue. If he is inexperienced he may just need some time to figure it out. If it doesn't seem to be working you can try hand breeding on a hill, I guess. How different in size are they?