This is quite hard to track down, as it is easy to see that there are excessive numbers of passengers generally, but there is no specific place where it is clear that the wrong number of passengers comes into existence at a specific time.
Further, it is very hard to test, as, once there are already excessive passengers, they will last for a long time, and the fast forward speed is very low on a large map with a very large number of passengers.
However, I have pushed what I think may be a fix to this, based on a problem detected in goods transfers in which goods would sometimes be duplicated when they were being transferred (e.g. 50t of goods being unloaded, resulting in 70t of goods at the stop). Having tested this for several hours, the number of passengers by at least some metrics seems slowly to be decreasing.
This will be in to-morrow's nightly build. I should be grateful if you could re-test to see whether this problem is abated with the new version. Thank you for the report.