You are right, by looking at the metric output you only have 1 file open, if you look at your filebeat log is there any stacktrace present? Is Filebeat generating any errors in the log?
I see that you are running 6.2.2, I know that we have fixed a few leaks in 6.3 and also in 6.4 did you try with the latest release of filebeat if you are running into the same issue?