Well, you are mixing different forms of energy here. If you are moving magnet trough coil you are generally making work, and not using kinetic energy of the magnet.
The case, where you will convert the kinetic energy of magnet will be following:
On ice surface (no friction) you have coil, and you slide magnet trough coil. In that case, the magnet will decelerate due to eddy currents. Due to induction some voltage will be induced and if you would connect the edges of coil some current will flow. So kinetic energy will be transformed into kinetic energy of charge carriers or "energy of current", I really don't know better term. Bear in mind, that electrons generally have quite high kinetic energy due to thermal movement, but in this instance we don't have to take that into account, since this energy doesn't transform.
In the case, where you are moving magnet with hand you are experiencing some force, and therefore you make some work. In that instance work is transformed into energy of the current and than after current flows into thermal energy of the wires.
The magnetic energy of coil will come into account only in other case, where we would have some current, which flows thru the coil, and we would suddenly stop that current. Then the magnetic field would generate some current for short period of time.
But in the case of moving magnet we are only converting work into moving of electrons. If we would use current to move magnet we would convert energy of moving electrons into work.