The fact that this is a voucher tenancy probably puts you in a better position. The HAP contract is the HUD-required written contract between your landlord and the housing authority. As the tenant you are not a party to the HAP contract; the written contract between you and your landlord is the lease. You can review the terms of the HAP contract at http://portal.hud.gov/hudportal/documents/huddoc?id=52641.pdf.
Utility responsibilities of the landlord and the tenant are listed on page 3 of the HAP contract. This is supposed to reflect the terms of the lease. The tenant portion of rent is reduced to compensate for tenant-paid utilities. By certifying that some or all utilities are paid by the landlord and then charging the tenant for them, the landlord is collecting a higher assistance payment than the program allows. This is a breach of the HAP contract and could rise to the level of fraud.
I'd recommend that you contact your caseworker at the housing authority to report this issue. The landlord owes overpaid subsidy amounts to the housing authority. The housing authority may or may not be required to reimburse you for the overpaid tenant share of rent.
Is this an arrangement to which you agreed in order to persuade the landlord to rent to you? That would weaken your position. In any case the landlord should be reported to the housing authority to prevent financial abuse of subsequent tenants and the program.