What kind of foundation if any and comb are you using? Natural foundationless comb tends to have smaller cells causing smaller bees, which have faster metabolism and shorter brood cycle time thereby being a natural deterent to varroa mite infestion. This might be a good thing.
Also, what genetic breed or strain of bees are they? some are smaller than others. I have 8 hives here and some hives have noticably smaller beesize than others, even on plastic foundation of the larger cell size.
When one tugs at a single thing in nature, he finds it attached to the rest of the world. John Muir