It sounds like you have setup using either tier 2 or tier 3 certification which requires a 2% minimum contribution with at leaset 1% from the employer.
Does it include anything other than basic salary such as bonus, overtime, commission etc? If it doesn't then you probably should be using tier 1 which does require a 2% minimum from the employer.
I would check the scheme rules to make sure your payroll software is setup correctly. The People's Pension should also be able to help you with checking how your scheme is setup.