Sorry, not sure what exactly happened and maybe problem not tied to PackageKit itself, but GNOME Software crashed after update. I've tried to manually press update on Flatpak app and crash happened after few seconds.

systemd-coredump[91376]: Process 91123 (gnome-software) of user 1000 dumped core.

                                               Stack trace of thread 91123:
                                               #0  0x00007f1165433930 gtk_widget_unparent (libgtk-3.so.0 + 0x3ac930)
                                               #1  0x00007f11652d751d gtk_list_box_remove.lto_priv.0 (libgtk-3.so.0 + 0x25051d)
                                               #2  0x00007f1165b52561 g_cclosure_marshal_VOID__OBJECTv (libgobject-2.0.so.0 + 0x12561)
                                               #3  0x00007f1165b71000 g_signal_emit_valist (libgobject-2.0.so.0 + 0x31000)
                                               #4  0x00007f1165b71123 g_signal_emit (libgobject-2.0.so.0 + 0x31123)
                                               #5  0x00007f1165200ba5 gtk_container_remove (libgtk-3.so.0 + 0x179ba5)
                                               #6  0x00007f1165439f88 gtk_widget_dispose.lto_priv.0 (libgtk-3.so.0 + 0x3b2f88)
                                               #7  0x00007f1165b556c6 g_object_run_dispose (libgobject-2.0.so.0 + 0x156c6)
                                               #8  0x0000559d5ba3e738 gs_updates_section_remove_all (gnome-software + 0x70738)
                                               #9  0x0000559d5ba3e7e9 gs_updates_page_load (gnome-software + 0x707e9)
                                               #10 0x00007f1165b53e2a g_closure_invoke (libgobject-2.0.so.0 + 0x13e2a)
                                               #11 0x00007f1165b7d303 signal_emit_unlocked_R.isra.0 (libgobject-2.0.so.0 + 0x3d303)
                                               #12 0x00007f1165b70f02 g_signal_emit_valist (libgobject-2.0.so.0 + 0x30f02)
                                               #13 0x00007f1165b71123 g_signal_emit (libgobject-2.0.so.0 + 0x31123)
                                               #14 0x0000559d5ba55aa6 gs_plugin_loader_job_actions_changed_delay_cb.lto_priv.0 (gnome-software + 0x87aa6)
                                               #15 0x00007f1165a62171 g_timeout_dispatch (libglib-2.0.so.0 + 0x54171)
                                               #16 0x00007f1165a61a9f g_main_context_dispatch (libglib-2.0.so.0 + 0x53a9f)
                                               #17 0x00007f1165ab3a98 g_main_context_iterate.constprop.0 (libglib-2.0.so.0 + 0xa5a98)
                                               #18 0x00007f1165a5ee73 g_main_context_iteration (libglib-2.0.so.0 + 0x50e73)
                                               #19 0x00007f116591bdfd g_application_run (libgio-2.0.so.0 + 0xdbdfd)
                                               #20 0x0000559d5b9f8cf9 main (gnome-software + 0x2acf9)
                                               #21 0x00007f116498f1e2 __libc_start_main (libc.so.6 + 0x281e2)
                                               #22 0x0000559d5b9f8dde _start (gnome-software + 0x2adde)

                                               Stack trace of thread 91124:
                                               #0  0x00007f1164a5da5f __poll (libc.so.6 + 0xf6a5f)
                                               #1  0x00007f1165ab3a36 g_main_context_iterate.constprop.0 (libglib-2.0.so.0 + 0xa5a36)
                                               #2  0x00007f1165a5ee73 g_main_context_iteration (libglib-2.0.so.0 + 0x50e73)
                                               #3  0x00007f1165a60a91 glib_worker_main (libglib-2.0.so.0 + 0x52a91)
                                               #4  0x00007f1165a8f402 g_thread_proxy (libglib-2.0.so.0 + 0x81402)
                                               #5  0x00007f1164b3d3f9 start_thread (libpthread.so.0 + 0x93f9)
                                               #6  0x00007f1164a68b53 __clone (libc.so.6 + 0x101b53)

                                               Stack trace of thread 91125:
                                               #0  0x00007f1164a5da5f __poll (libc.so.6 + 0xf6a5f)
                                               #1  0x00007f1165ab3a36 g_main_context_iterate.constprop.0 (libglib-2.0.so.0 + 0xa5a36)
                                               #2  0x00007f1165a61163 g_main_loop_run (libglib-2.0.so.0 + 0x53163)
                                               #3  0x00007f116595001a gdbus_shared_thread_func.lto_priv.0 (libgio-2.0.so.0 + 0x11001a)
                                               #4  0x00007f1165a8f402 g_thread_proxy (libglib-2.0.so.0 + 0x81402)
                                               #5  0x00007f1164b3d3f9 start_thread (libpthread.so.0 + 0x93f9)
                                               #6  0x00007f1164a68b53 __clone (libc.so.6 + 0x101b53)

                                               Stack trace of thread 91269:
                                               #0  0x00007f1164a6355d syscall (libc.so.6 + 0xfc55d)
                                               #1  0x00007f1165aae50c g_cond_wait_until (libglib-2.0.so.0 + 0xa050c)
                                               #2  0x00007f1165a32081 g_async_queue_pop_intern_unlocked (libglib-2.0.so.0 + 0x24081)
                                               #3  0x00007f1165a32206 g_async_queue_timeout_pop (libglib-2.0.so.0 + 0x24206)
                                               #4  0x00007f1165a92049 g_thread_pool_thread_proxy.lto_priv.0 (libglib-2.0.so.0 + 0x84049)
                                               #5  0x00007f1165a8f402 g_thread_proxy (libglib-2.0.so.0 + 0x81402)
                                               #6  0x00007f1164b3d3f9 start_thread (libpthread.so.0 + 0x93f9)
                                               #7  0x00007f1164a68b53 __clone (libc.so.6 + 0x101b53)

                                               Stack trace of thread 91127:
                                               #0  0x00007f1164a5da5f __poll (libc.so.6 + 0xf6a5f)
                                               #1  0x00007f1165ab3a36 g_main_context_iterate.constprop.0 (libglib-2.0.so.0 + 0xa5a36)
                                               #2  0x00007f1165a5ee73 g_main_context_iteration (libglib-2.0.so.0 + 0x50e73)
                                               #3  0x00007f115431164d dconf_gdbus_worker_thread (libdconfsettings.so + 0x664d)
                                               #4  0x00007f1165a8f402 g_thread_proxy (libglib-2.0.so.0 + 0x81402)
                                               #5  0x00007f1164b3d3f9 start_thread (libpthread.so.0 + 0x93f9)
                                               #6  0x00007f1164a68b53 __clone (libc.so.6 + 0x101b53)

Getting GNOME Software crashes here too. abrt won't complete the report, claims not enough info in stacktrace/coredump.

Aug 16 08:55:12 fedora systemd[1]: packagekit.service: Failed with result 'core-dump'. Aug 16 08:55:12 fedora systemd[1]: packagekit.service: Main process exited, code=dumped, status=11/SEGV Aug 16 08:55:12 fedora packagekitd[1432]: g_signal_emit_valist: assertion 'G_TYPE_CHECK_INSTANCE (instance)' failed Aug 16 08:55:12 fedora packagekitd[1432]: instance of invalid non-instantiatable type '(null)'