How to handle logstash with multiple config file?

I have almost 20 config files from different servers, each config file is creating to a separate index. How can I handle the config files here, I have placed all the config files in the /etc/logstash/conf.d/ folder and started the process, it behaves weird.
Need help to fix my problem.

It's impossible to help with so little information. In what way does it behave weirdly?

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