I can't speak to a specific issue or date, but the issue generically is simply that there are points where CN and CP freights can conflict with the GO trains' routing. On occasion, this happens.
There has been talk of building a flyover/under so that GO trains have a fool-proof route that freights can't ever block. However, no one flyover will remove all the points of conflict. A much cheaper solution would be for CP and CN to keep their freights out of the way, as there aren't actually that many freights using the Hamilton part of the line, but it isn't foolproof, as trains can stall or break down in the least desirable places. Plus, delays to freight trains are not readily accepted by the railways.
The only substantive change in recent times, other than the trains getting longer, is CP now regularly uses pusher engines to get these longer trains up the hill to Waterdown, and that adds to the number of movements over the CP part of the territory.
- Paul