There is a tiny electronics module in the cord-end that does some stuff including negotiating the charge rate with the computer and responding to the computer command to turn on the green or amber LED.
That section of the cord gets hot. It may be nothing except essentially, "wear".
However, if the Magsafe end seems free to rotate around the cord, that sometimes deteriorates into a short circuit in the cable-end, which can get quite hot right before it fails.
