Jonathan Thompson, II - Inconsistent data - please help reconcile!

The source used for this profile is:

Memorial of James Thompson, of Charlestown, Mass., 1630-1642, and Woburn, Mass., 1642-1682; and of eight generations of his descendants,” by Thompson, Leander, 1812-1896. 1n; Thompson Memorial Association. Page 22-23. https://archive.org/details/memorialofjamest00inthom/page/22/mode/1up

But RONALD B THOMPSON points out:

there is something that is inconsistent with the data.

Jonathan Thompson II married Francis Whitmore. They are listed to have twelve children. However, she passed in 1700 and and seven of the twelve children were born after 1700.

Records show that in 1700 Mary Boutwell married Jonathan Thompson II. I think it was 25 Mar 1700. I would assume the remaining children were hers. But, I checked several different sites and searches were she is list with just one child. She is Sarah Thompson born abt 1715. So, here is what I have for Jonathan Thompson II.

Francis Whitmore Married 1684
Jonathan Thompson b 1683 d 1752
Hannah Thompson b 1691 d 1791
Joseph Thompson b 1694 d 1755
James Thompson b 1696 d 1776
Susannah Thompson b 1699 d 1760

Mary Boutwell married 25 Mar 1700
Ebenezer Thompson b 1701 d 1755
Mary Thompson b 1703 d ?
Patience Thompson b 1713 d 1750
Sarah Thompson b 1715 d ? This is the only child she is listed to have had.
Jabez Thompson b 1716 d 1759
Esther Thompson b 1716 d 1777 I assume Esther and Jabez were twins
Daniel Thompson b 1718 d 1718 lived about 3 months.

Everything I find from various tree sites is this information. Then there is the written material that doesn't support my findings. I'm trying to determine what is correct.