Touch-up Factors

Color: Hue of the subsequent applied paint may be lighter or darker.
Sheen: Sheen or gloss development can be different; the touched-up area may be higher in sheen than the surrounding area, though it can be vice versa.
Profile: Touch-up can be noticeable depending on how much the re-applied paint is built up above the original paint as apposed to being flush and even.

Application at different temperatures: Touching up at significantly higher or lower temperatures than that of the original painting may make a difference.
Use of different methods of application (e.g., using a brush to touch up paint that was sprayed on).
Application over surfaces of differing porosity; for example, applying a satin paint to unprimed (porous) wallboard will result in a lower sheen than will develop with the same paint applied to itself when touching up.
Inadequate color acceptance (e.g., substandard compatibility between tinting color and the paint): The paint may develop a slightly darker color depending on shear stress applied to the paint by the act of applying it (shear from spraying > shear from brushing > shear from rolling).
Higher sheen paints (eggshell, satin, semigloss) tend to show sheen differences more than flats, with touch-up.

Apply an appropriate primer before painting.
Be sure the paint has been tinted properly (appropriate tinting base/colorant type/colorant level per gallon).
Some painters find it helpful to immediately backroll after spraying, to purposefully make a less uniform surface that touches up well with careful rolling.
Touch up within about 5°F of the original application temperature.
Do the touch-up in a thin application; a foam brush can be helpful for this, especially if the surface was originally sprayed. Slight dilution of the touch-up paint may be helpful. Never force dry the touch up.
Some painters pre-condition touch-up paint that was originally sprayed by spraying a quantity into a five gallon pail, then using that for touching up by use of a narrow foam roller or a foam brush. Use extreme care; wear eye, skin and breathing protection, and cover as much of the pail as possible with a heavy dropcloth while spraying the paint during conditioning.