Notice the green train westbound to the upper square station. Notice that it has star passengers on it. They should have transferred to the orange line at the previous station (triangle) and the seats thus vacated should have been filled by waiting circle passengers. (the output_log.txt file is from March, therefore useless).
Notice the plus passengers on the red train eastbound away from the square station and travelling away from the closest transfer station to a line going to the plus station.
Notice the blue train eastbound between the triangle and diamond stations. There are gem/cone (???) shaped passengers on this train, but the station of that shape is to the west. The previous triangle station would have been the most appropriate place for eastbound passengers to transfer. Given where they actually started, the shortest route for these passengers would have been to get on a westbound train and transfer at the football/rugby shaped station.
Notice the plus passenger on the yellow train moving away from the star station.
I wonder if track distance (or even simple station count) with an additional penalty for each transfer might not be the most efficient pathfinding method for passengers to unique stations.