Yes, it is inaccurate! I created it a long time ago, and I had initially not planned to write the Last Hours or any sequel series to The Infernal Devices. However, once I had the idea for the story, and the characters began to develop in my head, I knew I had to disregard the “family tree.” Otherwise I would have to write The Last Hours bound by a series of rules that were the opposite of story-generative — because when I created the tree, I hadn’t intended there to be a story. I’ve said for years that the family tree is inaccurate and not to look at it as a guide to what will happen in TLH, but I do know it’s never possible to reach everyone with that kind of information.
So, yes, the events of TLH don’t match the family tree, and that’s on purpose. The inaccuracy of the family tree is explained in-world (Esme Hardcastle!) but often people want to know if there will be a final family tree that’s accurate. After this experience, I can only say that I will only create a final family tree once I know I’m not writing another Shadowhunter book ever!