Yeah, I've found the same thing. Auto-attack is very aggressive and will equip any available weapon (or tool, if you have no weapons). You can select a non-auto-attack control mode in settings, but the auto-attack is the default and will sometimes revert when loading a saved game. If you, like me, want to keep auto-attack on, a workaround I use is keep a chest outside the hutch and drop all weapons and tools in there before entering. (The only exception to auto-attack aggression is when you want it to re-equip your weapon but instead you stand there like a fool with a handful of parsnips while the bats swarm you...anyway, that's a different story. My point is, auto-attack does not spare hutched slimes.)
