Keep right angles in line connecting objects in OmniGraffle
You need to make the line orthogonal. From OmniGraffle's "Drawing Basics" page:
To create an orthogonal line … , click the line to select it and use the Line inspector to change the line type to Orthogonal.
That will change the first line below into the second.
Right click on the line and select Add Midpoint to control precisely where those 90 degree turns will be.