I noticed these errors coming out of filebeat:
2016/03/25 15:34:30.198179 file_other.go:39: ERR Rotate error: rename /root/.filebeat.new /root/.filebeat: no such file or directory
2016/03/25 15:34:30.198234 registrar.go:105: ERR Writing of registry returned error: rename /root/.filebeat.new /root/.filebeat: no such file or directory. Continuing..
Googling, I found this issue against the obsolete logstash-forwarder (but which filebeat is based on): https://github.com/elastic/logstash-forwarder/issues/466
In my setup, I am running two instances of filebeat (both consuming from stdin for two different applications). From the above link, I am inferring that my errors are occurring because I am running both instances of filebeat in the same working directory, and the filename "filebeat.new" is not unique to each instance. I will confirm by running them in separate working directories.
I wanted to offer this up for discussion before submitting it as a defect/enhancement to be able to run multiple instances of filebeat from the same working directory.