If I have the mining drones set to collect wood, in addition to gathering the wood, they destroy the chute item from the Miniloader mod. It doesn't appear to happen with any other kind of resource.

can you provide a save game?

I've uploaded a simple save game here. Only these two mods enabled and the drones are heading right for the chutes.
https://ufile.io/07y35f6h

Well... the miniloader mod said that the chutes make wood when they're mined, so my guys are mining them for the wood

I see no reason why they need to be defined to say they make wood, I would suggest the issue is on the miniloader mod side of things

Thanks for looking.