This was mentioned again in #1339 but was closed and not fixed. My server has DNS records for both IPv4 and IPv6 connections and the OwnTracks app will choose the IPv6 address to connect to by default. If I delete the AAAA record it works just fine. The error in the logs is the following:
Caused by: java.net.ConnectException: failed to connect to mydomain.com/<Server's IPV6> (port 443) from /<Phone's IPV6> (port 57050) after 30000ms: isConnected failed: EHOSTUNREACH (Software caused connection abort)