Then did the little Maid reply, "Seven boys and girls are we; Two of us in the church-yard lie, Beneath the church-yard tree."
"You run about, my little Maid, Your limbs they are alive; If two are in the church-yard laid, Then ye are only five."
In these stanzas, the little girl is resolute. She repeats her words, telling the speaker that "two of us in the church-yard lie," and yet that they are "seven boys and girls." The girl has no doubts about her number of siblings.
As for the speaker of the poem—boy, does he have doubts. He argues with the cottage girl, saying that "if two are in the church-year laid"—i.e., if two are dead as doornails—that they are only "five" total (and not seven).
He's a little cruel in making his argument. He points out to the little girl that she can "run about," that her "limbs they are alive." This is in contrast to those siblings who are six feet underground.
This argument is really the crux of the poem: for the child, her siblings remain her siblings even after death.
For the speaker, once you are dead, you are no longer family. Hence the different math in the poem: she counts seven; he counts five.