To reproduce:
1. Open attached project
2. Build to iOS

Before the build finishes, some errors appear (they are pasted at the bottom of the description). Notice that one of those errors (in the second block of text) references UnityEngine.AndroidJavaClass, while this is an iOS build.

Reproduced on: 4.7.2f1
Not reproduced on: 5.1.4f1, 5.5.0b3

These are the errors that appear:

Failed running /Applications/Unity 4.7.2f1/Unity.app/Contents/Frameworks/Tools/UnusedByteCodeStripper2/UnusedBytecodeStripper2.exe -out "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed" -l none -c link -x "/Applications/Unity 4.7.2f1/Unity.app/Contents/Frameworks/Tools/UnusedByteCodeStripper/native_link.xml" -f "/Applications/Unity 4.7.2f1/Unity.app/Contents/Frameworks/il2cpp/LinkerDescriptors" -x "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/../platform_native_link.xml" -x "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/methods_pointedto_by_uievents.xml" -d "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed" -a "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/Assembly-CSharp.dll" -a "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/UnityEngine.UI.dll" -a "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/Tapjoy.Android.dll" -a "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/Tapjoy.iOS.dll" -a "/Users/benediktasl/Downloads/case_829755-tapjoy11test/Temp/StagingArea/Data/Managed/Tapjoy.dll"

stdout;
Fatal error in Mono CIL Linker
Mono.Cecil.ResolutionException: Failed to resolve UnityEngine.AndroidJavaClass
at Mono.Linker.Steps.MarkStep.MarkType (Mono.Cecil.TypeReference reference) [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.MarkField (Mono.Cecil.FieldReference reference) [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.InitializeFields (Mono.Cecil.TypeDefinition type) [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.InitializeType (Mono.Cecil.TypeDefinition type) [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.InitializeAssembly (Mono.Cecil.AssemblyDefinition assembly) [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.Initialize () [0x00000] in <filename unknown>:0
at Mono.Linker.Steps.MarkStep.Process (Mono.Linker.LinkContext context) [0x00000] in <filename unknown>:0
at Mono.Linker.Pipeline.Process (Mono.Linker.LinkContext context) [0x00000] in <filename unknown>:0
at Mono.Linker.Driver.Run () [0x00000] in <filename unknown>:0
at Mono.Linker.Driver.RunDriverWithErrorHandling (Mono.Linker.Driver driver) [0x00000] in <filename unknown>:0
at Mono.Linker.Driver.RunDriver (Mono.Linker.Driver driver) [0x00000] in <filename unknown>:0
stderr:

UnityEngine.Debug:LogError(Object)
UnityEditorInternal.Runner:RunManagedProgram(String, String, String, CompilerOutputParserBase)
UnityEditorInternal.AssemblyStripper:RunAssemblyLinker(IEnumerable`1, String&, String&, String, String)
UnityEditorInternal.AssemblyStripper:StripAssembliesTo(String, String, String&, String&, String, String, IEnumerable`1)
UnityEditorInternal.AssemblyStripper:Strip(String, String, String&, String&, String, String, IEnumerable`1)
UnityEditorInternal.AssemblyStripper:Strip(String[], String[], String, String, String&, String&, String, String, IEnumerable`1)
UnityEditorInternal.IL2CPPBuilder:RunAssemblyStripper(IEnumerable, String, String[], String[], String)
UnityEditorInternal.IL2CPPBuilder:StripAssemblies(IEnumerable`1, String)
UnityEditorInternal.IL2CPPBuilder:Run()
UnityEditorInternal.IL2CPPUtils:RunIl2Cpp(String, String, IIl2CppPlatformProvider, Action`1, RuntimeClassRegistry)
UnityEditor.HostView:OnGUI()

Error building Player: Exception: /Applications/Unity 4.7.2f1/Unity.app/Contents/Frameworks/Tools/UnusedByteCodeStripper2/UnusedBytecodeStripper2.exe did not run properly!