Sounds like the crank arm and wheel spokes don't overlap due to the small wheel size. If so, then you have two choices:

1: Change the laws of physics such that the magnetic field of one of the magnets is displaced sufficiently from its physical location to allow it to trigger the sensor.
2: Go with separately mounted cadence and speed sensors instead of a combination speed/cadence sensor.

I suspect option 2 will be more easily accomplished.