There can be many reasons why you could get this situation. The first thing to check is if the source line features are polyline Z and could it be the three edges meeting at that X,Y location have different Z coordinates. I am not sure when you say elevation is 0 if it was for the 3d coordinate or for the Z Levels that can also cause this. Or there can be a connectivity group policy in place.
You can add the network dataset to Pro and use the Explore Network tool (on the network dataset/data layer ribbon) and examine those edges to see if there is some you can figure out causing the two junctions.
Jay Sandhu