You are not running the config you think you are.
This is wrong, remove this line from your logstash.yml, this will tell logstash to run pipelines.yml as it was a logstash configuration file, which is not correct.
You should not have path.config in logstash.yml.
Just removing this line should solve the issue, but share both your logstash.yml and pipelines.yml to confirm this is the cause.