Thank you for opening the issue, I will poke engineering a bit tomorrow if I get a chance. When I asked before (as I ran into myself) I was told this will be fixed in / mitigated in a future release and at this point it is does not indicate any actual issues.
Is there any functionality other than the error message that is broken for you? If so let us know, otherwise I would proceed with the stack.
If you are using 7.11.1 and enable apache and / or ngnix and then run setup the correct ML jobs will be loaded.
I just built a brand new stack ...
$ ./filebeat modules enable apache nginx
$ Enabled apache
$ Enabled nginx
$ ./filebeat setup
......
Exiting: 3 errors: Error setting up ML for apache_ecs: 10 errors: ; ; ; ; ; ; ; ; ; ; Error setting up ML for apache_ecs: 10 errors: ; ; ; ; ; ; ; ; ; ; Error setting up ML for nginx_ecs: 10 errors: ; ; ; ; ; ; ; ; ;
I get the same error however when I go into Kibana the correct ML jobs are loaded for apache and nginx, my understanding is that is what would be broken if it was an actual issue.
