Depending on how fast you go, and how fast you can actually render the chunks, the speed the locomotives have usually are too much for the passenger cars themselves to handle. The entities (cars, freight, tender, locomotive, you name it) can also get duped across a relatively large map, after running for extended periods of time at speeds, say, over 50 mph. The problem starts at 40 MPH and is more common in Multiplayer, running under a dedicated server.

Steps to reproduce the unwanted behavior:

Grab 1 - 5 passenger cars, more if you want.

Get some villagers in. You'll need a good amount, so to see how bad the effects of it is, I'd say 20+.

Make sure you're in a dedicated server, have it able to render quite a few chunks to be safe, I usually use 20 on singleplayer, but better safe than sorry, you'll also need a locomotive that exceeds 100 MPH, prefereably steam since that is what I was using at the time.

Go as fast as possible with the villagers.

The expected outcome should be the tender/passenger cars phasing into and out of the locomotive, while at the same time the villagers should be out of the render distance, and without being checked on, they will most likely despawn, or just vanish due to how fast you are going. I would add screenshots, but a video would make more sense on it instead.

This runs under a server, but it runs under a Ryzen 9 5900X, 128GB of DDR4 ECC 2666Mhz, but the plan itself is 10GB.

latest.log

I guess the best way to fix it would to be that once entities are IN the passengers, even if fixing them "vanishing" out of sight is impossible or too complicated, it would register that those seats are taken and cannot be used with other villagers. Could go for players too in the future. I am also not on the latest test build, but this should theoretically be still present in other versions.

Here's the modlist in screenshots, I'd have to get a proper modlist from the server's owners themselves, sorry!

I just found out the hard way and discovered the bug too. On my dedicated server, after having 14 villagers vanish from a moving passenger train, I discovered two spots where I was hearing the villagers make their usual noises, but they were invisible. After a server restart, the invisible villagers would be gone.

My theory is that they're somehow getting kicked out of the passenger cars, it's weird.

EVEN at lower speeds the bug has happens on my end.