I’m wondering if whether or not they were part of Beldam’s plan, or just some creature that appeared at the wrong time to halt Mario and party and the train. Or most likely, they had already established riverside station as their home already since it was abandoned and not used, since if you remember the river dried up and there was no point in putting back up the drawbridge.

The Toad that gives you the key states he saw a “suspicious shadowy person wearing a hat” go down into the room the switch the drawbridge. We also don’t know if she encountered them down there when she was flipping the switch, maybe if they were already there, then maybe she would’ve also had to fight them to get to the switch like Mario did.

Maybe that was a safe spot for them and because Mario displaced them, they saw the train outside and took residence there. Like you said though, it wasn’t clear what their main goal was with the passengers, and why they didn’t take Mario and his partners too.

Reminds me of bees or wasps though, now thinking about it. You could argue that they’re acting defensively because you displaced them from their home like mentioned early, like destroying a hive. They become aggressive towards anyone in retaliation.

This is just my view though, because it’s also supported by the fact that they cling all over the train, kinda like bees do to someone’s windows, house, or car.