If you're a ca, your wage is £9.30 an hour, if you pay into a pension, provided you didn't alter the default amount, you pay 4.9% of your wages into it, 4.9% of £9.30 is 45.57p, the national living wage is £8.72.
In short, there are restrictions in place on what an employer can deduct from your wages if it brings your average earnings from hours worked to below minimum wage, i think pension contributions are one of the exceptions, but how they process it matters in that regard. I'd imagine similar restrictions apply to the cycle to work scheme.