Well, if the marriage and death certificate both say her mother was Isabella Fraser, you are pretty safe to assume that her mother was Isabella Fraser.
I can see exactly why they might have thought her mother was Margaret Sinclair, however. The transcription of the 1861 census at
http://www.freecen.org.uk/cgi/search.pl lists the family in Rathven
William Dick, 37, ironmonger, plumber, bell hanger, tinsmith etc
Margaret Dick, wife, 36, born Ordiquhill
Anne Dick, daughter, 12
Harriot Mary Stewart Dick, daughter, 6
Jessie Mabel Smith Dick, daughter, 3
Margaret Ann Dick, 1
all born Rathven except Margaret who was born in Ordiquhill.
The census index at SP lists Ann Dick, aged 2, in a household in Rathven with Elizabeth Dick, 66. Using the reference (ED1, page 11) I was able to scroll back and see that FreeCEN lists them as Pick! Elizabeth Pick, 66, widow, born Balvenie, and Ann Pick, granddaughter, aged 2, born Bogmoor.
Bogmoor is in on the right bank of the River Spey north of Fochabers. This is a slightly anomalous area, because sometimes it is enumerated in the parish of Bellie in Moray, and sometimes in the parish of Enzie in Banffshire. Enzie. Parts of Rathven are also sometimes enumerated in Enzie, so it can be confusing. See
http://www.abdnet.co.uk/genuki/BAN/Enzie/index.htmlIt's also useful to bear in mind that Enzie remained largely Roman Catholic when neighbouring parishes became Protestant, so it is always worth checking Roman Catholic records for anyone with a connection to Enzie.
Balvenie is just outside Dufftown, in the parish of Mortlach in Banffshire.
FreeCEN also lists in 1851 William Pick, 27, copper and tin smith, born Buckie, with wife Margaret, born Cornhill, Banffshire. Cornhill is in the parish of Ordiquhill.
In 1841 there is a household consisting of James Dick, copper smith; Elisbath Dick, 56; and Joseph Dick, 20, occupation transcribed as teetotaler and annotated 'age unclear'.
I recommend viewing the originals of all these censuses on SP to make sure that you check and decide for yourself any transcription errors!