It's not as complicated as it seemed at first- what's throwing us off is Eliza's maiden name.
To start with, there weren't that many Nugents in Trandragee (which may mean that they came from outside at some point) and there are only 2 Charles Nugents of concern- Charles (born 1875) and his father (born c1841). So, in the absence of other marriages (for a Charles Nugent to an Eliza O'Hanlon or Gilpin), the following is likely to be correct-
Charles Nugent (c1841-1906) m. Eliza Gilpin/McClean/O'Hanlon (c1838-1916)
The 1857 marriage date for Charles Nugent & Eliza McClean fits with the birth of eldest known child. In 1911 Eliza's granddaughter Mary Nugent (Charles, Jr.'s daughter) is staying with her
1. Elizabeth/Lizzie Nugent (c1859) m.(1887) James Campbell
This is likely the Lizzie Nugent informant for Margaret Nugent's death. That Margaret is probably a sister to Charles, Sr. and thus Lizzie Campbell's aunt. In 1911 the Campbells have Lizzie's nephew Thomas staying with them (Charles, Jr.'s son)
2. Thomas Nugent (c1861-1917) m.(1881) Ellen Toal
In 1911 neice Annie Nugent (Charles Jr.'s daughter) is staying in the household
3. Margaret Nugent (c1866) m.(1892) William Hagan
Marriage certificate confirms her father as Charles Nugent
4. Annie/Anna Nugent (1867-1897)
5. Mary Nugent (1870-1884)
6. Ellen Nugent (1872-1875?)
7. Charles Nugent (1875-1910) m.(1896) Annie Mackin (d.1907), m.(1908) Annie Hagney
I have seen parish records where the mother's maiden name was recorded (incorrectly) a few times and in each case I think the mother was from outside the priest's parish. It might even be that Eliza was known by several surnames (father's surname, mother's surname, stepfather's surname) which I've also seen happen in fairly recent times.
More to follow later...