In shiftfs, a non-upstream patch to the Linux kernel included in the Ubuntu 5.0 and 5.3 kernel series, shiftfs_btrfs_ioctl_fd_replace() installs an fd referencing a file from the lower filesystem without taking an additional reference to that file. After the btrfs ioctl completes this fd is closed, which then puts a reference to that file, leading to a refcount underflow.
