The marshalling in was also incorrect.

modules/mono/mono_gd/gd_mono_marshal.h

@@ -201,7 +201,7 @@ Dictionary mono_object_to_Dictionary(MonoObject *p_dict);
 	m_in.origin.x, m_in.origin.y, m_in.origin.z                    \
 };
 #define MARSHALLED_IN_Transform(m_in, m_out) Transform m_out(                                   \
-		Basis(m_in[0], m_in[1], m_in[2], m_in[3], m_in[4], m_in[5], m_in[6], m_in[7], m_in[8]), \
+		Basis(m_in[0], m_in[3], m_in[6], m_in[1], m_in[4], m_in[7], m_in[2], m_in[5], m_in[8]), \
 		Vector3(m_in[9], m_in[10], m_in[11]));
 
 // AABB