It's not got any code for dealing with ores specifically. Just trees get special cased. And when trees that give items other than wood get mined, the other items get dropped on the ground.
What's happening is that it isn't picking up on the changed ore, and thinks it still has a valid mining target of the original type, then finding that it isn't picking up the original type and dumping it.
Could you check if issuing the commend "mining-depots-rescan" makes it stop dumping Deep Core ores on the ground until another square gets depleted? This isn't a fix, just information gathering.
Also, should mining drones be able to mine the Deep Core ore?