"3 phase" Type of winding I am not aware of, help? not wye or delta, maybe eFed up generator?
The fact that you have magnets implies a brushless motor, and wye configuration is the most common.  In motors, the number of magnet poles does not really correlate to the number of phases.  The only real requirement is that the magnet poles must be even in number.  If you are running a ten-pole motor, the magnet arrangement will be identical after each one-fifth of a revolution (72 degrees).  At this point, the north and south poles will be re-aligned in the same way they were when the revolution started, so you will need five complete phases to get one revolution.  You can find the term "electrical revolution" in some of the literature;  In your case, it requires 5 electrical revolutions to make one mechanical revolution.  So your generator output frequency will be five times higher than you would get with a two-pole generator run at the same speed.  This is desirable in some cases to keep the rpms low.

Illustrations of brushless motors often show the most simple arrangement of windings and magnets so that they are easy to understand, but in practice the number of poles and the number of slots in the stator are arranged in a manner to provide the desired back emf waveform - most often sinusoidal or trapezoidal - so that they can be driven with a minimum of torque and current ripple.  For instance, we manufacture 8-pole motors with 21 or 27 slots in the stator.  A slot in the stator has windings from two of the three phases and the wind would certainly seem random to many, but it is really only complex.  I am guessing your motor is just fine.

Good luck!