A workaround for this type of thing is sometimes to just run your request multiple times. Some validations will work each time and so they won't be re-attempted next time (valid authorizations are cached for approx 30 days), eventually all the validations will pass and the certificate order will complete.
The real fix is probably to investigate the problem with your DNS provider API so you can set multiple values.
Alternatively you could:
- switch to a major DNS provider (e.g. cloudflare, AWS Route 53, Google Cloud DNS etc)
- use a DNS challenge delegation service (acme-dns https://github.com/joohoi/acme-dns, or Certify DNS which is a managed version of roughly the same idea and is provided by my organization: Certify DNS | Certify The Web Docs)