The magnetic field of a star is not entirely a result of the global spin of the star. The global spin is part of it, but there are other mechanisms as well. Within the star, there are convection zones, meridional flow, etc.
http://solarscience.msfc.nasa.gov/dynamo.shtml
All these flows generate their own field components. The overall field is simply the sum of all little fields. Its general orientation might be close to the global spin, if the strongest components are aligned to it, but there are many smaller components with different orientations. Therefore, the total field of the star can be somewhat slanted.
And then the star collapses into a neutron star, and its field is compressed. The collapse itself may be slightly asymmetrical, and may further deviate the magnetic field axis.
As a result of all of the above, it's by no means unusual that the magnetic field of the neutron star is not aligned with the spin.
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