Some waypoints are connected incorrectly in some rooms, for example, in "testroom" Waypoints are connected to each other, this is displayed in game with the red lines you see with wireframe on.
In this room, 096 is trying to reach the player by using the path that goes between the railing of each side. The game though this was possible since the two waypoints can "see" each other, however NPCs can't actually use this path.

A way to solve this would be adding an invisible object that prevents some waypoints from seeing each other.