It is done on purpose. You have to make sure the signal is only cleared once.

Fun map, but I've encountered an issue: train 911, when stopped at Llandudno Junction platform 4 actually says it is stopped at a signal, and I got penalised for it. I tried switching the signal on and off and every time I switched it off I got penalised for stopping at the signal (while the train is waiting at the platform). Could it be the train is too long for the platform?