No. The joint filing service is an optional addition to HMRC's online filing software. If you choose not to use the joint filing service or you're encountering difficulties, it's important to make sure you still comply with the Companies Act requirements. You should check your filing deadline and submit accounts to Companies House direct, using the options available from the Companies House WebFiling service.
You can get further advice by contacting Companies House on 0303 123 4500.