Under the Display options, there is an option to show close vertices. This utilises an auto scale based on the bounding box of the model to determine whether vertices are close to each other, otherwise the user can put in a manual value. When you have the rectangular box included in the model, the total bounding box is significantly increased. The yellow lines are drawn between the vertices that Mechanical is detecting as close. If you are happy with your geometry, you can simply turn off the option to display close vertices.n