Either at random or through some weird thing (possibly boats), carts change layers from 4 to 2, causing it to vanish under the dirt. Their pixel_y value also changes from 0 to something else, usually a number in the 20's.

When getting off of a boat, turning, and dragging the cart onto the player, the cart changes layers as well as changes whatever verb the cart/boat checks when looking at if the cart is already in a boat or not. So essentially, when trying to drag said cart back onto a given boat, it will pop up with, "That cart is already on a boat.".

I'm not sure if this is actually covered in AJ's post, but from what I've observed, sometimes carts that are experiencing the layers bug will (disappear?) completely.