I spotted the following lines:
It seems there is something strange happening with the registrar. Not sure if this could be a problem related to access rights to the registry file. Could you remove the registry file and start filebeat from scratch again to see if you get the same output?
When you refer to logs: Are you referring to 4096 log files or log lines? If log files, I'm thinking if there could be an issue with ulimit and the maximum of file handler that can be opened.
How often does pfsense rotate the log file? As you report the issue happens on startup, this "should" not have an impact I would think but it is good to know.
For debugging: The above is perfect. There is also and option logging.level: debug for the config file which could be used. For larger outputs feel free to also post a link to a gist.