I experienced something similar before in Elastic APM 6.5.3 (Docker version) when I was using custom RUM transactions. It disappeared when I upgraded to 6.6.0.
The symptom on my side is that the Service name appears in the APM home page, the transactions and traces names appear in the drill down (when you click on the service name), but when the traces and transactions are clicked for details, it returns an empty page. The transactions and traces can be viewed in Discover page.
As mentioned above, it only affected my custom RUM transactions. As I am using 6.6.0 now, i can no longer reproduce the symptoms.