I think that I may have fixed this, but it is hard to tell, as the problem is complex. The immediate problem was caused by a huge number of pedestrians being generated when a huge packet of passengers at one stop decided that it would be quicker to walk than take the train/'bus. However, this does not tell me what caused there to be such a huge number of passengers (many tens of thousands) in the first place. I have altered the pedestrian generation algorithm to set it to generate a maximum of 128 at a time, which should at least prevent the game from crashing or becoming unresponsive in this state, but that is not a fix for the problem itself. The errors that you are reporting in the log, incidentally, are likely to be an effect, rather than a cause, of the problem: these excessive delta_t instances occur when the game is bogged down.
I have also pushed a fix to what I think that the ultimate cause of the problem probably is, and this should now be available on the current nightly build. I think that this was a bizarre instance of extra passengers being generated on transfers due to an iterator fault, similarly to a near identical problem reported with goods some time ago. I have pushed a fix to this (which worked for goods), and some preliminary tests suggest that this may have worked, but it is hard to be sure without having a specific instance where the problem can be tracked down without doubt.
I should be grateful if you could let me know whether there appears to be any improvement with this.