Both endpoints either have configuration in /etc/icinga2/zones.d or in a deployed api config package which uses zones.d. I would guess that you’ve used the Director to deploy its package against both REST APIs. You can only do this for one endpoint, with a manual failover to the secondary host.
In order to clean things up, delete the director config package on the second master endpoint. This can be done with a curl request as explained in the API docs for Icinga 2.
Cheers,
Michael