The disappearing passengers are a known issue, which means that it’s maybe getting fixed some day.
As for the train not fully loading: It is moving out again. Did those passengers already wait at the station while the train loaded? Passengers sometimes seem to come in groups; if the train has finished loading and a bunch of people arrive, they may have to wait for the next one.
At least that’s the only explanation I can think of; I never noticed happening that there were 88 people waiting when the train arrived, and it took only 73 of them and left the rest.