I read through the report earlier. As usual Network Rail aren't painted in a good light; especially when you read about similar incidents, on the same line, in the last few years. The subject of User Worked Crossings (UWC) is always a subject of safety discussion. Looking at the report one of the factors examined was signaller workload, something identified after a previous incident.
Another issue is where the signalling is absolute block - a train could be anywhere within that block section and neither signaller may fully know the exact whereabouts. They rely on the honesty of the crossing user. There are still also cases where a user crosses without permission.