I was having the following issue:
 - the node had the correct environment set in puppet.conf
 - the node was in the right environment in foreman
 - I ran puppet on the node and in foreman it was moved to the default environment

I've noticed that in my setup the /opt/puppetlabs/server/data/puppetserver/yaml/node/$fqdn.yaml is not getting generated (yaml/facts/$fqdn.yaml is there). 
I don't know why it doesn't get generated but it seems that upgrading to puppet 5 that file stopped being written.

As pointed out by gwmngilfen, the above file is used in the classifier script in case the environment is not amongst the facts ( https://github.com/theforeman/puppet-foreman/blob/master/files/external_node_v2.rb#L119-L130 )

Currently the variable `name` which defines the environment is  follows ( https://github.com/theforeman/foreman/blob/develop/app/services/puppet_fact_parser.rb#L64 )
<pre>
    name = facts[:environment] || Setting[:default_puppet_environment]
</pre>

I have disabled "ENC environment" setting (because I want the agent to be able to specify a different env for testing features). So I'm not sure how the behavior should be in case the setting is enabled but a simple workaround for this would be
<pre>
   name = facts[:environment] || facts[:agent_specified_environment] || Setting[:default_puppet_environment]
</pre>

I tested the above on 1.15.2 and it works as expected.