Well spotted! I did search for existing reports but obviously I didn't get the right combination of keywords to find that. I suppose I would still have needed to post this as it is still broken.

I used an upgrade planner to replace efficiency modules 3 with speed modules 3 in an assembler, but cancelled the upgrade using control+Z while the bots were mid-flight (after collecting the speed modules, but before reaching the machine). The bots returned the speed modules to a storage chest ...