About half of the Thunderstone Ore generated by striking lightning on exposed Stone via field move will turn into Cobblestone as if it's just normal Stone, despite giving off a light source as if it's normal Thunderstone Ore.
1. Use a Pokemon that has the Lightning Bolt field move to strike some exposed Stone, turning it into Thunderstone Ore.
2. Attempt to mine the ore. About 50% of the time, this will act as if it's normal Stone and drop Cobblestone.
I have provided a link to an unlisted video demonstrating this. https://www.youtube.com/watch?v=hl95X9wK9Qk