major drills asked me to delete three items from my inventory.

I thought it would be a drag to find the item, click it, chose delete and go back to my inventory three times, so I went to quickstock and deleted all three simultaniously from there. I refresh drills again and the delete counter is still at 0/3

Is this a bug?

You specifically have to delete them from your inventory menu for it to count (i.e. go to inventory > click on item > click delete). I'm not sure why it was setup that way and deleting from your shop is excluded, but that is why he doesn't just ask you to delete items but to delete them from your inventory in the instructions.

It's probably the same reason why you can't just delete pumpkins through quick stock to get the "Delete 1000 pumpkins" achievement: it's meant to take more effort.