Occasionally referencing mistakes are made (i.e. a Marked Point is referenced to a Marked Point on another photograph but they do not correspond to the same point on the object) and are not noticed right away. At some later time, when trying to reference some other Marked Points, the connecting lines appear to be wrong or PhotoModeler will not allow two Marked Points to be referenced that are clearly the same point on the object.
The easiest way out of this problem is to select what you think to be the incorrectly referenced points, and choose "Unreference Selected Points" from the right click menu (or Create Tab‘s Referencing Group’s Expand menu). Once the points are unreferenced start referencing them again taking special care to reference correctly.
If the project is small or you have not proceeded far in the referencing stage you can select all points on all photographs and unreference all of them. This gives you a clean slate to start over again with referencing.