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If you place them by hand the magnets are off by a little bit. You could use applescript to place them exactly.

The coordinately system places the object center at 0,0 and scales the object to a size of 1.


Code:
-- select an objects to add magnets to in omnigraffle

-- these are examples lists of points for each edge of an object 
-- the two corners and the middle each get a magnet

set left_edge to {{-0.5, -0.5}, {-0.5, 0}, {-0.5, 0.5}}
set right_edge to {{0.5, -0.5}, {0.5, 0}, {0.5, 0.5}}
set bottom_edge to {{-0.5, 0.5}, {0, 0.5}, {0.5, 0.5}}
set top_edge to {{-0.5, -0.5}, {0, -0.5}, {0.5, -0.5}}

tell front window of application "OmniGraffle Professional"
	
	-- this will add magnets to all selected objects
	set objects to selection
	
	repeat with obj in objects
		set magnets of obj to left_edge
	end repeat
end tell