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.
Variables that can cause or contribute to touch up problems
Application at different temperatures: touching up at significantly higher or lower temperatures vs. 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 (i.e., sub-standard 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, semi-gloss) tend to show sheen differences more than flats, with touch-up.
Tips for avoiding touch-up problems
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 purposely make a less uniform surface that touches up well with careful rolling.
Touch up within about 5° 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 5 gallon pail, then using that for touching up by use of a narrow foam roller, a foam brush, etc.; 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.