Use Preview Bounds

By default, Illustrator uses the path of an object for measurements, alignments, etc., ignoring the stroke width. No matter how thick the stroke, the size of the object will be measured based on the position of the path. If you want to use the stroke width (and position) as the reference rather than the path, press Command-K (PC: Control-K) to go to the Preferences dialog and check Use Preview Bounds. From then on, all operations will be measured based on the thickness and position of the stroke, as shown here in the Transform palette (Window>Transform).