Per the IGI, Margaret Anne Parfitt's mother was Margaret (Skelly) not Martha.
Margaret died March 1875 and John married Martha in 1876.
The census in 1881 shows Margaret Anne as the daughter, but that is her relationship to John (Joseph) as head of the household.
In 1891 she is shown as the daughter of Martha (John not being present), but I suspect that she was really the stepdaughter, but treated as Martha's daughter. The post 1881 children are obviously those of Martha.