A day, i.e. 24 hours, isn't how long the Earth takes to rotate. It's the time between the Sun being in the same place in the sky, but that isn't the same as the time it take the Earth to rotate 360° because the Earth moves around the Sun at the same time as rotating on its axis. Strictly speaking what we call a day is a solar day.
The time the Earth takes to rotate by 360° is called a sidereal day, and it's 23 hours, 56 minutes and 4.1 seconds i.e. about 3.9 minutes less than a solar day. The period of a geostationary satellite is a sidereal day not a solar day, and that's why it too is 3.9 minutes shorter than a solar day.
If you are interested in reading more about this you'll find lots of articles about sidereal time on the web. I found a good introductory article on the Astronomy Essentials web site.