Reproduction Steps:
1. Import attached project.
2. Wait until all jobs are done.
3. Close Unity.

Result: Unity crashes.

Stack trace:
0x0000000140E12AA2 (Unity) MonoScript::BelongsToEditorCompatibleAssembly
0x0000000140E1F0F4 (Unity) MonoScriptManager::FindRuntimeScript
0x0000000140E1F18D (Unity) MonoScriptManager::FindRuntimeScript
0x000000014149FEC5 (Unity) MonoBehaviour::StartCoroutineManaged2
0x00000001414A00AE (Unity) MonoBehaviour::CheckConsistency
0x0000000141077340 (Unity) AwakeFromLoadQueue::InvokePersistentManagerAwake
0x000000014107AC79 (Unity) AwakeFromLoadQueue::PersistentManagerAwakeFromLoad
0x000000014107AE66 (Unity) PersistentManager::IntegrateAllThreadedObjects
0x000000014107F670 (Unity) PersistentManager::LoadAndIntegrateAllPreallocatedObjects
0x000000014107F90E (Unity) PersistentManager::ReadObject
0x00000001400309E7 (Unity) PPtr<MonoBehaviour>::operator MonoBehaviour * __ptr64
0x0000000140883A41 (Unity) HasInvalidBehaviourPredicate::operator()
0x000000014078593D (Unity) std::remove_if<PPtr<MonoBehaviour> * __ptr64,HasInvalidBehaviourPredicate>
0x00000001414D458B (Unity) AnimatorState::CheckConsistency
0x0000000141077340 (Unity) AwakeFromLoadQueue::InvokePersistentManagerAwake
0x000000014107AC79 (Unity) AwakeFromLoadQueue::PersistentManagerAwakeFromLoad
0x000000014107AE66 (Unity) PersistentManager::IntegrateAllThreadedObjects
0x000000014107F670 (Unity) PersistentManager::LoadAndIntegrateAllPreallocatedObjects
0x000000014107F90E (Unity) PersistentManager::ReadObject
0x0000000140031127 (Unity) PPtr<AnimatorState>::operator AnimatorState * __ptr64
0x00000001414DD548 (Unity) AnimatorStateMachine::CheckConsistency
0x0000000141077340 (Unity) AwakeFromLoadQueue::InvokePersistentManagerAwake
0x000000014107AC79 (Unity) AwakeFromLoadQueue::PersistentManagerAwakeFromLoad
0x000000014107AE66 (Unity) PersistentManager::IntegrateAllThreadedObjects
0x000000014107F670 (Unity) PersistentManager::LoadAndIntegrateAllPreallocatedObjects
0x000000014107F90E (Unity) PersistentManager::ReadObject
0x0000000140031867 (Unity) PPtr<AnimatorStateMachine>::operator AnimatorStateMachine * __ptr64
0x00000001412E605B (Unity) AnimatorControllerLayerToMono
0x00000001412D84D6 (Unity) VectorToScriptingClassArray<AnimatorControllerLayer,MonoAnimatorControllerLayer,std::vector<AnimatorControllerLayer,std::allocator<AnimatorControllerLayer> > >
0x00000001412EDECF (Unity) AnimatorController_Get_Custom_PropLayers
0x000000003B98F70D (Mono JIT Code) (wrapper managed-to-native) UnityEditor.Animations.AnimatorController:get_layers ()
0x000000003B98F109 (Mono JIT Code) [C:\buildslave\unity\build\Editor\Graphs\UnityEditor.Graphs\Animation\LayerControllerView.cs:146] UnityEditor.Graphs.LayerControllerView:ResetUI ()
0x000000000B3850F9 (Mono JIT Code) [C:\buildslave\unity\build\Editor\Graphs\UnityEditor.Graphs\Animation\AnimatorControllerTool.cs:332] UnityEditor.Graphs.AnimatorControllerTool:OnInvalidateAnimatorController ()
0x0000000013ADD2A8 (Mono JIT Code) [C:\buildslave\unity\build\Editor\Graphs\UnityEditor.Graphs\Animation\AnimatorControllerTool.cs:16] UnityEditor.Graphs.AnimatorControllerCallback:OnInvalidateAnimatorController (UnityEditor.Animations.AnimatorController)
0x0000000013ADD545 (Mono JIT Code) (wrapper runtime-invoke) <Module>:runtime_invoke_void_object (object,intptr,intptr,intptr)
0x000007FEE4645737 (mono) [c:\buildslave\mono\build\mono\mini\mini.c:4937] mono_jit_runtime_invoke
0x000007FEE4598435 (mono) [c:\buildslave\mono\build\mono\metadata\object.c:2623] mono_runtime_invoke
0x00000001410645B5 (Unity) scripting_method_invoke
0x0000000141059DF1 (Unity) ScriptingInvocation::Invoke
0x00000001407E91D0 (Unity) AnimatorController::InvalidateAnimatorController
0x0000000140906113 (Unity) MessageHandler::HandleMessage
0x0000000140906468 (Unity) SendMessageDirect
0x0000000140E0ACDC (Unity) UserList::SendMessageA
0x0000000140E0C19F (Unity) UserList::SendMessageA
0x000000014077F8BB (Unity) AnimationClip::MainThreadCleanup
0x000000014090C609 (Unity) delete_object_internal_step1
0x000000014090C802 (Unity) delete_object_internal
0x0000000141485280 (Unity) CleanupAllObjects
0x00000001414856EE (Unity) CleanupEngine
0x00000001401436E8 (Unity) AssetInterface::Shutdown
0x00000001417187B8 (Unity) Application::CoreShutdown
0x000000014171DA1F (Unity) Application::Terminate
0x00000001417D790C (Unity) ContainerWindow::ContainerWndProc
0x0000000076CC9C11 (USER32) TranslateMessageEx
0x0000000076CC72F7 (USER32) SetWindowTextW
0x0000000076CC6839 (USER32) IsDialogMessageW
0x0000000076DFBA75 (ntdll) KiUserCallbackDispatcher
0x0000000076CC686A (USER32) IsDialogMessageW
0x0000000076CC68B2 (USER32) IsDialogMessageW
0x0000000076CC763A (USER32) SetWindowTextW
0x000007FEFB4D795A (uxtheme) DrawThemeParentBackground
0x000007FEFB4F637A (uxtheme) Ordinal69
ERROR: SymGetSymFromAddr64, GetLastError: 'Attempt to access invalid address.' (Address: 000007FEFB4D168E)
0x000007FEFB4D168E (uxtheme)
ERROR: SymGetSymFromAddr64, GetLastError: 'Attempt to access invalid address.' (Address: 000007FEFB4D1445)
0x000007FEFB4D1445 (uxtheme)
0x0000000076CC89F7 (USER32) GetWindowDC
0x00000001417D7DB2 (Unity) ContainerWindow::ContainerWndProc
0x0000000076CC8995 (USER32) GetWindowDC
0x0000000076CC72F7 (USER32) SetWindowTextW
0x0000000076CC6839 (USER32) IsDialogMessageW
0x0000000076DFBA75 (ntdll) KiUserCallbackDispatcher
0x0000000076CC686A (USER32) IsDialogMessageW
0x0000000076CC68B2 (USER32) IsDialogMessageW
0x0000000076CC763A (USER32) SetWindowTextW
0x000007FEFB4D795A (uxtheme) DrawThemeParentBackground
0x000007FEFB4F6425 (uxtheme) Ordinal69
ERROR: SymGetSymFromAddr64, GetLastError: 'Attempt to access invalid address.' (Address: 000007FEFB4D168E)
0x000007FEFB4D168E (uxtheme)
ERROR: SymGetSymFromAddr64, GetLastError: 'Attempt to access invalid address.' (Address: 000007FEFB4D1445)
0x000007FEFB4D1445 (uxtheme)
0x0000000076CC89F7 (USER32) GetWindowDC
0x00000001417D7DB2 (Unity) ContainerWindow::ContainerWndProc
0x0000000076CC9C11 (USER32) TranslateMessageEx
0x0000000076CC992A (USER32) TranslateMessage
0x00000001417F0A59 (Unity) CrashCallback
0x00000001417F2704 (Unity) WinMain
0x0000000141AD7444 (Unity) strnlen
0x0000000076BA59BD (kernel32) BaseThreadInitThunk
0x0000000076DDA2E1 (ntdll) RtlUserThreadStart

Note #1: Crash doesn't happen consistently after a few successful reproductions.

Reproducible with: 5.6.1p2, 2017.2.0a2
Not reproducible with: 5.5.3p4

Note #2: Because of the inconsistent reproductions, it's difficult to pinpoint the exact version the regression begins in.