I'm experiencing similar problems. This occurred on v5 and continues to happen on 6.0.1, on both SMB and AFP.
This is definitely happening on my end; however, Plex isn't running a scan during the process (auto-detect is turned off).
During prolonged access, as noted by the OP, if I try to navigate within the unRAID and/or copy a file, the Finder crashes and the unRAID webgui becomes inaccessible until a forced restart (I typically can telnet in, but the powerdown script hangs).
When I remember to, my workaround is to disconnect whenever I'm done with an activity and reconnect when necessary. But, this is less than ideal, especially since I typically forget.
Any updates or suggestions?