Wait were you still able to get through the whole game without sending the crates along ink trails?? Puzzlescript doesn't have a great way of showing information, so I'm not sure how to better get the idea across.
I think you've made some changes since I first played it, but the only ones that now seem to force using that mechanic are the level that introduces it and 'Out of the way'. Even so, the puzzles are still super fun!
I hear ya on the limitations of puzzlescript text, but maybe something like 'Press X to push a crate along an ink trail' communicates the idea better?