Well passing a signal at danger (WITH AUTHORITY) is a fairly regular occurance on the railway, although that's not to say that it's taken lightly. Since the signalling system is designed to be Failsafe, then any sort of problem would/should result in an errant signal staying at danger - hence the signaller authorising you to pass it at danger. There is a whole wodge of Rulebook dedicated to this since you've now abandoned the safety of the system.
I've had a moderately similar experience to the one mentioned above a while ago. I was waiting at a junction signal. After a train went past on the adjacent line which I was expecting cross over onto, my signal went to yellow, then red, then two yellows, then red, then two yellows again. This is classified an irregular signal sequence since a signal should never revert to a lesser aspect (unless of course the signaller 'puts back' on you for an emergency).
So I called the signaller and he said..
"O yes that's quite alright, I know what's causing that, don't worry"
To which the reply had to be
"Well I do, would you care to share it with me"
He explained that there was a problem with the points 'bouncing'. He was using ARS (Automatic Route Setting) and the computer had set the route as quickly as possible after the other train cleared the overlap. Points and signals are interlocked, so that the signal can't clear until the route is set and checked. As soon as the proving on the points saw them reverse it set the signal, but when the points bounced a bit the proving was removed and so the system put the signal back to danger. This happened several times quickly but there's always a little delay in the system so that I was treated to a bit of a light show.
This proving is an arrangement whereby the signalling system gets confirmation that things are how they should be. So there are sensors on the points to confirm that they are in the right postion. Similarly many colour light signals have proving on their bulbs. If a bulb burns out the signal in its rear will automatically step down to a single yellow at best, so that you automatically bring the train to a stand at the signal which isn't diplaying any aspect.
And finally we come to the reason for all this blather...... if a signal has an intermediate fault on the proving circuit, that can cause the signal to return to danger every time the proving is lost. But that's OK, as we all know that any signal which isn't showing a steady proceed aspect is automatically defined as being at danger.
Phew, HTH
Foggy