I think the problem is that along the main road, your template drop is (say) every 20m - so the main road finds the ground at points 20m apart, and joins them with a striaght line.
Your junction template is finding a point almost halfway between the two points found by the main road template. The existing ground could have a small hill at this position - which will be missed by the main road templates - which is picked up by the civil cell.
The simplest method to get the two to match up more accurately is to make your main road template drops a smaller value - say 5m. Another option would be to add a special chainage (key station) drop at the end of the junction arc to the main road to get a template added at that position to see the effect.