It looks like from the death records there was a third Benjamin died age 23, doesn't have his birth shown. Records of Births, Marriages and Deaths in the Town of Malden, Massachusetts 1649-1850, University Press, Cambridge, MA (Google it)
Malden Births (p. 102)
Whittemore, Benjamin, s. Benjamin, Jan. ––, 1667. CC
Whiitemore, Benjamin, s. Benjamin, 2: 9m: 1670. CC
Malden Deaths (p. 391)
Whittemore, Benjamin, s. Benjamin, Mar. 31, 1668. CC
Whittemore, Benjamin, s. Benjamin, ––: 10m: 1676. CC
Whittemore, Benjamin, Jr., [23 y.], Oct. 7 [Oct. 6. GS], 1703.
Whittemore, Benjamin [86 y.], July 16, 1726.