Steps to reproduce:
1. Open attached project "prefab_instantiation.zip"
2. Open Build settings, add "test" scene and build WSA Universal 10 SDK (or any WSA SDK)
3. Open VS solution
4. Deploy on local machine
5. Press any key
Result: player crashes when trying to instantiate a UI prefab into another UI prefab: Assertion failed on expression: 'hierarchy.transformChangedMask[index] == 0

Reproducible with .NET and IL2CPP scripting backends

Reproducible with: 5.4.0f3, 5.4.3p3, 5.5.0p1, 5.6.0b1

Callstack:
UnityPlayer.dll!Transform::ValidateHierarchyRecursive(TransformHierarchy & hierarchy, int & hierarchyOrderIndex, int & nextIndex, int parentIndex, unsigned char * hasTransformBeenVisited) Line 1891 C++
UnityPlayer.dll!Transform::ValidateHierarchyRecursive(TransformHierarchy & hierarchy, int & hierarchyOrderIndex, int & nextIndex, int parentIndex, unsigned char * hasTransformBeenVisited) Line 1905 C++
UnityPlayer.dll!Transform::ValidateHierarchy(TransformHierarchy & hierarchy) Line 1850 C++
UnityPlayer.dll!CollectAndProduceGameObjectHierarchy(Transform & root, Transform * newParent, vector_map<int,int,std::less<int>,stl_allocator<std::pair<int,int>,1,16> > & remappedPtrs) Line 142 C++
UnityPlayer.dll!CollectAndProduceClonedIsland(Object & o, Transform * newFather, vector_map<int,int,std::less<int>,stl_allocator<std::pair<int,int>,1,16> > & remappedPtrs) Line 204 C++
UnityPlayer.dll!CloneObjectImpl(Object * object, Transform * newFather, vector_map<int,int,std::less<int>,stl_allocator<std::pair<int,int>,1,16> > & ptrs) Line 259 C++
UnityPlayer.dll!CloneObject(Object & inObject, Transform & newFather, bool worldPositionStays) Line 336 C++
UnityPlayer.dll!Object_CUSTOM_Internal_CloneSingleWithParent(void * data_, void * parent_, int worldPositionStays) Line 42 C++
UnityEngineDelegates.dll!_Object_CUSTOM_Internal_CloneSingleWithParent@16() Unknown
1ccde3a6() Unknown
[Frames below may be incorrect and/or missing]
1ccde288() Unknown
1ccde131() Unknown
1ccde0c1() Unknown
1ccde080() Unknown
1e54502d() Unknown
1e544fa2() Unknown
1c75a1a0() Unknown
003ed236() Unknown
UnityPlayer.dll!metro_invoke_method(ScriptingMethodDotNet method, WinRTScriptingObjectWrapper object, ScriptingArguments * arguments, WinRTScriptingObjectWrapper * exception, bool convertArgs) Line 66 C++
UnityPlayer.dll!scripting_method_invoke(ScriptingMethodDotNet method, WinRTScriptingObjectWrapper object, ScriptingArguments & arguments, WinRTScriptingObjectWrapper * exception, bool convertArgs) Line 802 C++
UnityPlayer.dll!ScriptingInvocation::Invoke(WinRTScriptingObjectWrapper * exception, bool convertArguments) Line 288 C++
UnityPlayer.dll!ScriptingInvocation::Invoke() Line 80 C++
UnityPlayer.dll!MonoBehaviour::CallMethodIfAvailable(int methodIndex) Line 462 C++
UnityPlayer.dll!MonoBehaviour::CallUpdateMethod(int methodIndex) Line 561 C++
UnityPlayer.dll!MonoBehaviour::Update() Line 566 C++
UnityPlayer.dll!BaseBehaviourManager::CommonUpdate<BehaviourManager>() Line 153 C++
UnityPlayer.dll!BehaviourManager::Update() Line 171 C++
UnityPlayer.dll!`InitPlayerLoopCallbacks'::`2'::UpdateScriptRunBehaviourUpdatestruct::Forward() Line 1501 C++
UnityPlayer.dll!PlayerLoop() Line 173 C++
UnityPlayer.dll!metro::MainLoop(bool performRendering) Line 202 C++
UnityPlayer.dll!UnityPlayer::AppCallbacks::DoPerformUpdateAndRender() Line 1306 C++
UnityPlayer.dll!UnityPlayer::AppCallbacks::PerformUpdateAndRender() Line 1262 C++
UnityPlayer.dll!UnityPlayer::AppCallbacks::_AppThreadImplementation(void * param) Line 180 C++
UnityPlayer.dll!UnityPlayer::AppCallbacks::_AppThread(void * param) Line 212 C++
UnityPlayer.dll!win32::CreateThread::__l2::<lambda>(Windows::Foundation::IAsyncAction ^ __formal) Line 276 C++
UnityPlayer.dll!Platform::Details::__abi_FunctorCapture<void <lambda>(Windows::Foundation::IAsyncAction ^),void,Windows::Foundation::IAsyncAction ^>::Invoke(Windows::Foundation::IAsyncAction ^ <__args_0>) Line 881 C++
UnityPlayer.dll!Windows::System::Threading::WorkItemHandler::Invoke(Windows::Foundation::IAsyncAction ^ __param0) C++
UnityPlayer.dll!Windows::System::Threading::WorkItemHandler::[Windows::System::Threading::WorkItemHandler::__abi_IDelegate]::__abi_Windows_System_Threading_WorkItemHandler___abi_IDelegate____abi_Invoke(Windows::Foundation::IAsyncAction ^ __param0) C++
threadpoolwinrt.dll!Windows::System::Threading::CThreadPoolWorkItem::CommonWorkCallback() Unknown
threadpoolwinrt.dll!Windows::System::Threading::CThreadPoolWorkItem::TimeSlicedCallback(void *) Unknown
kernel32.dll!@BaseThreadInitThunk@12() Unknown
ntdll.dll!__RtlUserThreadStart() Unknown
ntdll.dll!__RtlUserThreadStart@8() Unknown