
Given that the "mother" Elizabeth Graham was married to Sir William Graham of Gartmore, 1st Baronet who only had one son (named John) I've disconnected that relationship.
I've changed DOB and DOD of William Graham to 1535-1618
These are the dates shown in FamilySearch and FindAGrave, neither give any sort of evidence or mention any sources but at least they look viable compared to the wife and daughter.
Hopefully someone with an interest and ability in this era will eventually do some proper research but for now the inconsistency warnings are resolved.