Honestly, you can ‘headcanon’ the disappearing passengers by imagining they’re passengers that got caught by a conductor and didn’t pay a ticket. If they’re not paying their 4k to travel to the next town, they might as well not exist. It doesn’t excuse the bug, but it gives it a semi-plausible explanation.
As for the main topic of this thread: Does the line stop at the same platform in both directions? As Stonelouse said, the people left on the platform might just look to travel the other direction. It’s the only plausible explanation, barring a very unfortunately timed bus unloading 15 people right as the train left.