Not sure if it's specific to the tendril explusion recipe, but that's what triggered it. Steps to reproduce:

• Have a folding engine with the tendril expulsion recipe set
• Put the cube in it (with less than 20k tendrils, not sure if there's a -minimum requirement, but I did it just now with 12k)
• Walk away
• Use remote view to change the recipe
• Cube and tendrils end up in the trash slots
• Mod starts spitting warnings about the cube being lost

Picking it up out of the trash slot stops the warnings. I noticed that it didn't apply the slowdown effect for a second or two, presumably when it -would- have given another warning.

Definitely not just expulsion: I also ran into this by having one folding engine toggle between separating and reconstituting via circuit signals. After splitting the cube, the recipe switches, the phantom cubes end up in trash output, and there are repeated console warnings until they're all emptied.