Have you run into a rotation puzzle and the nodes seem to jump more than you rotated or a node that moves isn't the node that is highlighted?
Rotation Puzzle Bug
The solution is very simple, albeit annoying, just reload the last save. It's not because intelligence is too low, if it was the game doesn't let you even attempt the puzzle. You do not have to reload very far back, any previous auto save will work even if its after the bug occurred.