Ok, that explains the issue. Unfortunately is not so difficult to end up with a wrong template, so I couldn't say how it happened. Maybe setup.template.enabled was false, maybe someone changed it, maybe some issue with upgrading/downgrading versions, maybe because of Kafka or Logstash output (if you are using one of those)
To fix it you should load the bundled template. If you are using Elasticsearch output, you can do it with apm-server -e setup template, otherwise https://www.elastic.co/guide/en/apm/server/7.3/_manually_loading_template_configuration.html provides a good explanation.
Keep in mind that changes will be effective for future indices only, not the existing ones.
Hope that helps!