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I was just starting a new v0.17 trying to do Lazy Bastard.

After getting some coal, iron and copper I pick up my stone furnace and drill and put the drill on a stone ore patch. At that moment, the stone furnace in my inventory CHANGES to a mining drill!!!
At that moment I still had 0 (ZERO) items crafted by hand. I used /permissions to disable 'craft'.

Here are the 2 saves (one autosave before the pickup, and one manual save after placing the drill).

Cannot reproduce. Try disabling your mods.

But you can see in the save game itself that I did not craft a single item yet? That means it definitely shouldn't happen (impossible in fact). I had the same bug again, but this time with an assembling machine 1. After creating and using 1 machine, I picked it up and saw there were 2 assembling machine 1's in my inventory.

Twice now my Lazy Bastard run has been ruined.
Could it be a bug with /permissions craft? I've not had this happen before (previously I simply changed the 'craft' key bindings to something ridiculous so that I wouldn't accidentally craft something).

You're probably running a mod that makes it so you can place entities without removing them (or at least one of them) from your inventory. As Bilka said, test this with all mods disabled.