That might be happening due to vehicle spacing system.
If there are 2 buses near each other, the bus in the back will use the station to wait more time and increase the space between them, balancing the distance in the line.
I'm not sure but I think the opposite also happens. If the bus is at the station and another bus is coming behind, this bus will leave the station faster than normal.
Also the game runs slow, like in real time. It does takes some time to stop, to passengers get in and out and leave again. Specially if you have old ladies boarding. Just be patient with them, could be your grandmother.
That cannot be the cause of crowed stations. If you have crowed stations search for another solution: increase bus capacity, divide the route in 2 or more lines, change the type of transportation (tram for example).
Choosing the optimal type of transport and the optimal vehicle (speed or capacity) is one of the game challenges.
I think you guys are talking about two different things.
The problem claimed by vonhaubitz is happening to me right now (it's not the first time, but currently i'm unable to handle it).
After a huge improvement of one of my metro lines (i've added like 4 stations), an interchange station (one stop of line 1) started to be overcrowded. Nothing i can normally handle, there were like 300 people, two new trains would be enough. But, as told, it was an interchange station, and after the improvements it became the main metro line, so people were increasing fastly. I can count an average increase of 30/35 people per (game) day. Still manageable.
However, when the first train reached the station, it happened. 192 of 200 were inside the train (within 2 game-days), for remaining 8 people the game spent almost 8 game-days, so for 8 people the station crowd increased by 200. Especially last one (when the train was 199/200) spent a lot of time.
It creates traffic jams, my metro stop have reached 1100 people within minutes, and now i'm afraid it compromised all my game (Leipzig, 10 years), because i have, at the moment, like 5 trains (of 33) in queue waiting for that damn 1 person (199/200). When the train approachs the station, waiting people are 1100. When it leaves, waiting people are 1150. And so on.....
Is it a game bug? Is it possible to solve in some way, maybe editing some value in the scripts?