I've had some stops with hundreds of angry people waiting. I've had metro stations with 1500 angry people waiting. And it's a compliment that what I've built so far makes them dead keen to use my network, but it isn't quite balanced enough for their entire journey to go smoothly and efficiently.
And it's VITAL information to help with planning how to improve and extend, by showing me where the bottleneck is. Why on earth do you want them to go away? Then you'd get no fares or income! If they use their cars, they'll make the whole journey in them, so they won't use the metro or tram that's probably associated with the queue. And if the queue is at a railway station, then you will need more separate bus lines, or a tram, or metro to cope.
Sometimes the queue will clear if you add enough big buses to the line. But this might just shift the waiting queue to the next linking line, which also then needs more vehicles, etc....
But if it persistently stays more than 100, then it's a signal you really need a tram or metro going to or from that location, because it's too popular for a bus. If the queue is because a metro is depositing many more passengers than the local link can handle, then consider building more and smaller dispersal bus lines from that location.
Add a second bus line (using a separate stop also covering the delivering station, perhaps even just across the road) and each stop only gets half the passengers. This system can handle twice as many buses, but it's important that the bus lines don't impede each other. The finite load/unload time is the killer for just throwing more buses at one line, and having multiple lines all using the same single stop won't help in the slightest. When the buses are queuing up at the stop, and 100's of angry passengers can't get on fast enough, that's the biggest signal there is that the single bus line/stop is inadequate.
So plan an alternative. Build a tram dispersal instead of a bus line. Or multiple trams - make use of the default twin track build. Or extend the metro a bit further so that some passengers use the next stop instead.
Like douglasrac said, the game is telling you something, and it's up to you to learn how to use that info. If you'd prefer them to go away and use their cars instead, then why are you trying to build a public transport network? You'll make no money without them. I'd rather have a queue of 500 angry passengers as an "advance order book", than one or two happy people causing my line to run at a loss, and telling me to cut the service instead of where to grow.
I've just finished Paris, carrying thousands of passengers each month, and while I hit over 500 red, angry, waiting passengers at some stops at one point, I saw that as a target to plan for, and it took YEARS before my "solution" arrived. And I was very glad the game persisted with a huge, angry queue, because it encouraged me to keep going with my plan. If the simulation made them go away, how would I have known where to target the metro to? The finished network had every stop with green, happy faces and no more than 50 people waiting anywhere. I was playing on "hard", didn't use any dlc vehicles to make it even harder, was making about $8k profit each month on a $40k turnover, had ramped all vehicle maintenance up to 95%, stop maintenance to 60%, had happy employees, and bus and tram fares in "green". Immensely satisfying. And buses tended to be only used for a few dispersal / catchment zones in the low density suburbs. I had trams covering the denser suburbs.
My worst ever situation (Vienna, I think) took four attempts at rebuilding, replanning and redirecting trams and buses at a three-way linkup to stop them impeding each other, or just causing local traffic jams. But once I got it right, the red angry queues melted away in a few months as the lines ran smoothly and unobstructed.
It took me quite a few scenarios before I even had a clue how to deal with these sort of problems. Now, it's sometimes easy, sometimes a challenge, but I know it's ALWAYS resolvable. And I LIKE to see big queues build up because it's a sign that I've built something desireable that will make money and profit. Ka-ching. All those passengers just waiting to throw money at you..... yes please, let me at them....
Broken? I really don't think so...... As far as I can see, there's nothing to fix.
