Control Tower that the parent organizational unit is not enrolled in AWS Control Tower, when it is

Ok so it's unclear how you are programmatically create new account.

However, I'm assuming you are using the Service Catalog API, as specified here.

Please make sure the ManagedOrganizationalUnit field has the specific format of OU_NAME (OU_ID)

As seen below:

{
  pathId: "lpv2-7n2o3nudljh4e",
  productId: "prod-y422ydgjge2rs",
  provisionedProductName: "Example product 1",
  provisioningArtifactId: "pa-2mmz36cfpj2p4",
  provisioningParameters: [
    {
      key: "AccountEmail",
      value: "abc@amazon.com"
    },
    {
      key: "AccountName",
      value: "ABC"
    },
    {
      key: "ManagedOrganizationalUnit",
      value: "Custom (ou-xfe5-a8hb8ml8)"
    },
    {
      key: "SSOUserEmail",
      value: "abc@amazon.com"
    },
    {
      key: "SSOUserFirstName",
      value: "John"
    },
    {
      key: "SSOUserLastName",
      value: "Smith"
    }
  ],
  provisionToken: "c3c795a1-9824-4fb2-a4c2-4b1841be4068"
}