On an Ubuntu 14.04, I have started to receive the following warning (or error) each time I start a new session in terminal :
Unable to make or open a FIFO for universal variables with path '/run/user/0/fishd.12c79b706e7a.notifier': Permission denied
When I try to look into this file, the file does not exist at all.
This is fish issue #2222.
The problem seems to be that you get the wrong value for $XDG_RUNTIME_DIR. In that issue the reporter said su -l caused it, which, unlike what the documentation said, did not clear $XDG_RUNTIME_DIR or set it again to the wrong value.
I get a much more benign issue on fish 2.2.0 (and current git):
fish: No TTY for interactive shell (tcgetpgrp failed)
setpgid: Inappropriate ioctl for device
which seems not to break anything, so I can only recommend upgrading.