Yes I cannot believe that damn family tree still haunts me but here is the compilation of all the known discrepancies in the family tree (thus far)
Feel free to add more if I missed something
Contains spoilers for Chain of Gold
1) Cordelia Carstairs’ actual mother is Sona Turan (Chain of Gold), not Colette Verlac (Family Tree)
2) Tatiana Lightwood was born in 1857 in the family tree whereas she was described to be younger than both (born in 1862) Gabriel and Gideon in A History of Notable Shadowhunters and Denizens of the Downworld
3) Lucie Herondale’s birthday was supposed to be around 1887 (one year younger than James according to Chain of Gold and The Whitechapel Fiend) as opposed to be 1891 (in which case she would’ve been 12 in Chain of Gold which does not make sense)
4) The year in which Edmund Herondale and Linette Owens died of influenza is 1899 (Chain of Gold), different from the family tree (1893 and 1895 respectively)
5) Elias Carstairs was said to be deceased in 1894 (Family tree), when he was clearly still alive in Chain of Gold (1903)
6) Barbara Lightwood died in Chain of Gold (1903), the family tree said she died in 1917, and in Clockwork Princess she might’ve been still alive by the epilogue (1937)
7) Baby Carstairs is completely absent on the family tree