After the pull. The parent hash points to ToT. But the graph points to completely different parent.

Similarly, after a hard-reseting a branch which is lagged from master to a more recent point in the master branch (but not ToT). The git tree graph no longer preserves the parent-child relationship of the submission

In the attached picture. You can see the high-lighted submission's parent is 0bc15cd170 (which is the top of the blue branch). But this is not reflected in the graph.

I want to add that by clicking the link in the submission text, it in fact jump to the right parent. So its only the tree graph is not right.