Loads of
--47513:1:VG_(fcnt fcntl error 9 Bad file descriptor
messages

This is due to

init_preopened_fds_without_proc_self_fd()

   for (i = 0; i < count; i++)
      if (VG_(fcntl)(i, VKI_F_GETFL, 0) != -1)
         ML_(record_fd_open_named)(-1, i);

The loop will result in one message per file that does not exist. On my RPi FreeBSD rlimit open files is 231219 and indeed I do see 231214 messages.

I'll turn off logging for that loop.