Data going into wrong index-why

Elastic Stack Logstash
2

If you are putting the two .conf files into the same directory and pointing logstash -f to that directory, then it concatentes the files, reads all the inputs, applies all the filters to all the events, and then sends the events to every output.

You can make the output conditional on the tags.

output {
 if "foo" in [tags] {
  elasticsearch {
    index => "this"
    ....
  } else {
   elasticsearch {
    index => "that"
    ...
  }
}