As others have said the new paint does not match the old paint well enough to blend. It can be very difficult to blend in non-glossy sheens as well. Glossy, Semi-Gloss are easier to match. Egg Shell and Matte/Flat can be very tricky, more so with darker colors.

One thing that can really help do a better cover-up job is not painting any straight lines. Paint a star pattern * around the cover-up, and fade the points out by by using less pressure on the brush. You want to use as little paint as possible for the patch. The idea is to avoid making and sharp transitions from one color to another.

One last note about color. Even using the same exact bucket of paint from one day to the next may cause color differences. This is often not noticeable with white and light colors, but with darker (and flat-sheen) colors you should expect more problems.