This issue appears to be fixed: it no longer reproduces for me with macOS 10.12.6.  I suspect it was caused by the same underlying behavior change to poll described here: https://github.com/curl/curl/issues/1057 (fixed in 10.12.2).

This only appears on MaxOS 10.12.

I'm seeing the same thing, here is the stack trace as reported by Apple's crash reporter:

3   libsystem_c.dylib                     0x00007fffc9447893 __assert_rtn + 320
4   xargs                                 0x0000000100e02e9f complain_about_leaky_fds + 145
5   xargs                                 0x0000000100e014f3 xargs_do_exec + 532
6   xargs                                 0x0000000100e024f5 bc_do_exec + 248
7   xargs                                 0x0000000100e00c7d main + 3117

This change avoids the crash by not checking the file descriptors for stdin, stdout or stderr, but tbh I can't follow all of what's going on in there:

diff -ur findutils-4.6.0/lib/fdleak.c findutils-4.6.0.patched/lib/fdleak.c
--- findutils-4.6.0/lib/fdleak.c        2015-12-29 08:10:23.000000000 +1100
+++ findutils-4.6.0.patched/lib/fdleak.c        2016-11-22 14:47:29.000000000 +1100
@@ -294,7 +294,7 @@
   context.used = n;
   context.lookup_pos = 0;
   context.leaked_fd = -1;
-  visit_open_fds (0, max_fd, find_first_leak_callback, &context);
+  visit_open_fds (3, max_fd, find_first_leak_callback, &context);
   return context.leaked_fd;
 }

I hope that helps,
Michael.

[sunrunaway:~]$ echo a | /usr/bin/xargs > /dev/null 2>&1 ; echo $?
0
[sunrunaway:~]$ echo a | /usr/local/bin/xargs > /dev/null 2>&1 ; echo $?
125