It does seem to be a "feature", and not something to worry about. I don't think you are doing anything wrong. Missed passengers always seem to get on the next vehicle.
I agree that sometimes the numbers defy logic, sometimes leaving ten passengers behind when the vehicle has room for 20 more. And I'm convinced that some of those left behind were already waiting at the stop. But the next vehicle along does always seem to pick everyone up, and I've given up trying to work out the logic behind it.
It isn't even clear whether it is the passenger's choice which vehicle to board, or if the approaching vehicle triggers a decision point whereby it knows who will be getting off, how much room there will be, and who (from the waiting queue) will be getting on. I don't think it decides while stationary at the stop, or simply wait for a defined time length. The decision is made well before the vehicle comes to a halt. The "granny" passengers with zimmerframes walking from the back of the platform can force a stop length three times longer than usual, so the vehicle is waiting for specific passengers to board.
For me, this problem seems to occur when I've just added new vehicles to a line. I know that a new vehicle will immediately leave the first stop without waiting for anyone to board. But it is almost as if the vehicle is ignored by passengers that were already waiting many stops ahead. Like those passengers already knew which vehicle they would board when they arrived at the stop, and ignore any extra ones that arrive early. But this is all speculation on my part. Only CO know for sure how this boarding decision logic is programmed. It's just one of those mysteries we have to accept as it is.