Cannot reproduce here.

Operating system: Linux-4.15.0-55-generic-x86_64-with-debian-stretch-sid 64 Bits
Blender: 2.80 and latest master

Please check if the problem has been fixed for you since 2.80:

• Download the latest build from http://builder.blender.org.
• Go to File → Defaults → Load Factory Settings and then load your file to see if you still can reproduce this issue.

Well, I'll post an update whenever either the 2.81 download finishes (it's been going for about 2 hours now, previous attempts have timed out) or the build I just started finishes.

In the meantime, here's a video of it happening with default settings in 2.80 final:

Good news, does not appear to be happening on the build I just made- so it may have been fixed by something else. I'll hammer on it for a bit longer and see if I can get it to break

Scratch that- not happening in edge mode, but I was able to repro it in face mode. Since I went through the trouble of building Blender I went ahead and made a debug build to get a callstack, this is the output:

blender.exe!issue_debug_notification(const wchar_t * const message) Line 28
at minkernel\crts\ucrt\src\appcrt\internal\report_runtime_error.cpp(28)
blender.exe!__acrt_report_runtime_error(const wchar_t * message) Line 154
at minkernel\crts\ucrt\src\appcrt\internal\report_runtime_error.cpp(154)
blender.exe!abort() Line 61
at minkernel\crts\ucrt\src\appcrt\startup\abort.cpp(61)
blender.exe!CustomData_get_layer_index(const CustomData * data, int type) Line 2065
at c:\blender-git\blender\source\blender\blenkernel\intern\customdata.c(2065)
blender.exe!CustomData_has_layer(const CustomData * data, int type) Line 2509
at c:\blender-git\blender\source\blender\blenkernel\intern\customdata.c(2509)
blender.exe!bpy_bmesh_dealloc(BPy_BMesh * self) Line 3452
at c:\blender-git\blender\source\blender\python\bmesh\bmesh_py_types.c(3452)
[External Code]
blender.exe!BPY_DECREF_RNA_INVALIDATE(void * pyob_ptr) Line 583
at c:\blender-git\blender\source\blender\python\intern\bpy_interface.c(583)
blender.exe!WM_operator_free(wmOperator * op) Line 78
at c:\blender-git\blender\source\blender\windowmanager\intern\wm.c(78)
blender.exe!WM_operator_stack_clear(wmWindowManager * wm) Line 184
at c:\blender-git\blender\source\blender\windowmanager\intern\wm.c(184)
blender.exe!ed_undo_exec(bContext * C, wmOperator * op) Line 389
at c:\blender-git\blender\source\blender\editors\undo\ed_undo.c(389)
blender.exe!wm_operator_invoke(bContext * C, wmOperatorType * ot, wmEvent * event, PointerRNA * properties, ReportList * reports, const bool poll_only, bool use_last_properties) Line 1451
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(1451)
blender.exe!wm_handler_operator_call(bContext * C, ListBase * handlers, wmEventHandler * handler_base, wmEvent * event, PointerRNA * properties) Line 2279
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(2279)
blender.exe!wm_handlers_do_keymap_with_keymap_handler(bContext * C, wmEvent * event, ListBase * handlers, wmEventHandler_Keymap * handler, wmKeyMap * keymap, const bool do_debug_handler) Line 2581
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(2581)
blender.exe!wm_handlers_do_intern(bContext * C, wmEvent * event, ListBase * handlers) Line 2718
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(2718)
blender.exe!wm_handlers_do(bContext * C, wmEvent * event, ListBase * handlers) Line 2977
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(2977)
blender.exe!wm_event_do_handlers(bContext * C) Line 3464
at c:\blender-git\blender\source\blender\windowmanager\intern\wm_event_system.c(3464)
blender.exe!WM_main(bContext * C) Line 420
at c:\blender-git\blender\source\blender\windowmanager\intern\wm.c(420)
blender.exe!main(int argc, const unsigned char * * UNUSED_argv_c) Line 493
at c:\blender-git\blender\source\creator\creator.c(493)
[External Code]

Here's a video of it happening in face mode with the latest from git.

Please clarify what you mean by "committing the operation" and "undo without committing the operation".

committing the operation- when the operator is no longer running modal and has returned. in other words- while the operator panel with all of the operator properties is still visible.

Furthermore, please prepare a new file in which you can reproduce the crash with as few steps as possible

I'll try, but as you can see in the video above it's happening on the default cube with factory defaults restored. Not sure how much simpler I can make it than that :)

Cannot reproduce either here on linux with current master. Your crashlog is weird too, since it seems to go through py API of bmesh when freeing operator, that does not make much sense as bevel is a C op… What is the operator in the WM_operator_free() call in that stack when the crash happen?