This has to do with fetch options/progress callbacks being reclaimed too
early.  The backtrace upon segfault looks like this:

--8<---------------cut here---------------start------------->8---
(gdb) bt
#0  0x00007f83dc798a3e in get_callee_vcode (thread=thread@entry=0x7f83dbe2fd80) at vm.c:1499
#1  0x00007f83dc7a08a4 in scm_call_n (
    proc=proc@entry=<error reading variable: ERROR: Cannot access memory at address 0xe0>0xe0, 
    argv=argv@entry=0x7ffe6426d200, nargs=2) at vm.c:1606
#2  0x00007f83dc729fcc in invoke_closure (cif=0x7f83cbbfc580, ret=0x7ffe6426d420, args=0x7ffe6426d270, data=0xe0)
    at foreign.c:1100
#3  0x00007f83dc463ed1 in ffi_closure_unix64_inner ()
   from /gnu/store/bw15z9kh9c65ycc2vbhl2izwfwfva7p1-libffi-3.3/lib/libffi.so.7
#4  0x00007f83dc464800 in ffi_closure_unix64 ()
   from /gnu/store/bw15z9kh9c65ycc2vbhl2izwfwfva7p1-libffi-3.3/lib/libffi.so.7
#5  0x00007f83c6e452a1 in do_progress_callback (stats=stats@entry=0xd843c0, idx=<optimized out>, idx=<optimized out>)
    at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/indexer.c:562
#6  0x00007f83c6e457cb in git_indexer_append (idx=0xdc3930, data=<optimized out>, size=<optimized out>, 
    stats=0xd843c0) at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/indexer.c:809
#7  0x00007f83c6e9c6df in git_smart__download_pack (transport=0xda08a0, repo=<optimized out>, stats=0xd843c0, 
    progress_cb=0x7f83d8da50b8, progress_payload=<optimized out>)
    at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/transports/smart_protocol.c:582
#8  0x00007f83c6e7a15b in git_remote_download (remote=remote@entry=0xd842f0, refspecs=refspecs@entry=0x0, 
    opts=opts@entry=0x7ffe6426d808) at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/remote.c:989
#9  0x00007f83c6e7ae0e in git_remote_fetch (remote=0xd842f0, refspecs=refspecs@entry=0x0, 
    opts=opts@entry=0x7ffe6426d808, reflog_message=reflog_message@entry=0x0)
    at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/remote.c:1025
#10 0x00007f83c6e909d9 in git_submodule_update (sm=0xd81360, init=1, _update_options=<optimized out>)
    at /tmp/guix-build-libgit2-1.1.0.drv-0/libgit2-1.1.0/src/submodule.c:1352
#11 0x00007f83dc46466d in ffi_call_unix64 ()
   from /gnu/store/bw15z9kh9c65ycc2vbhl2izwfwfva7p1-libffi-3.3/lib/libffi.so.7
#12 0x00007f83dc462ac0 in ffi_call_int () from /gnu/store/bw15z9kh9c65ycc2vbhl2izwfwfva7p1-libffi-3.3/lib/libffi.so.7
#13 0x00007f83dc72a33e in scm_i_foreign_call (cif_scm=<optimized out>, pointer_scm=<optimized out>, 
    errno_ret=errno_ret@entry=0x7ffe6426dc9c, argv=0x7f83ce7d7880) at foreign.c:1073
--8<---------------cut here---------------end--------------->8---

To be continued…

Ludo’.