I am using the most recent version of the pack at the time of writing, I think. It seems like just taking an item from the inventory system has a chance of duping it! After a bit of testing it seems like this is caused by an interaction between a trim and a create chute, as removing it seems to stop this from happening.
More specifically, I have a setup with two gold chests stacked on top of each other with a chute in between, all of that connected to the inventory system with trims.

Tom's is unfortunately abusable, and this isn't the first dupe that's been found. The mod has been updated and claims to fix some dupes so we'll see what happens in 1.1.13