JMX integrations such as Cassandra, Tomcat, Kafka, etc. can potentially generate thousands of metrics, by default the JMX based Integrations are limited to 350 for licensing purposes. Any number above 350 will be counted towards your custom metric limit.
Accepting arbitrarily large numbers of metrics is not a concern for Datadog, the limitation is in place purely for licensing issues so as to not negatively impact your billing. If you'd like this number increased please email email@example.com.
To check the current metric list, run the JMX list_everything command that is provided via the agent:
sudo /etc/init.d/datadog-agent jmx list_everything
To list attributes that do match one of your instances configuration but that are not being collected because it would exceed the number of metrics collected:
sudo /etc/init.d/datadog-agent jmx list_limited_attributes