Reproduce:

$ mkdir /tmp/a.dir

$ mkdir /tmp/b.dir

$ mkfifo /tmp/a.dir/afifo

$ mkfifo /tmp/b.dir/afifo

$ diff -r /tmp/a.dir /tmp/b.dir

File /tmp/a.dir/afifo is a fifo while file /tmp/b.dir/afifo is a fifo