Is anyone else seeing an issue where the workcarts are noclipping through some (not all) entities on tracks?

Which entities?

Does this happen to all workcarts or only the automated ones?

If you unload the plugin, and spawn new workcarts, does it happen to them as well?

In general, there should not be other entities on the tracks. Some servers were having a problem where automated workcarts would be stopped by junkpiles and loot containers that would spawn along roads, but the most recent update to the plugin resolves that by destroying such obstructions, not by no clipping through them.

I unloaded AutomatedWorkcarts and it was still happening with standard spawns and the plugin unloaded. It looks like it might've been a custom map issue.

Do you have any other plugins which affect train cars? Some of the ones recommended for custom maps, such as TrainRustEdit and WorkcartSpawner, can affect train car collision.

No, the map creator I use suggests your plugin.