One thing I do is set the home person back to before or just above the point where the families cross each other. this might help you temporarily, but is no permanent fix.

Surely they considered this issue when creating program? I wish they would put a disclaimer pop up on the feature telling people it does not work if your family lines cross.

Actually, mine do not cross, just touch with one minor remote marriage of third cousins and it is enough to throw the whole descendancy list supplied by AMT out of whack.