I just want to add, that this isn't just a woodcutter related issue. You can craft the misbehaving stone blocks from any crafting menu into andesite, diorite or granite. I also have the issue and have both regular and misbehaving stone. I cannot confirm if my misbehaving one comes from cooked cobblestone but it is very likely, although it is not systematic. I also have stone from furnaces that behaves normally.
I just want to add, that this isn't just a woodcutter related issue. You can craft the misbehaving stone blocks from any crafting menu into andesite, diorite or granite. I also have the issue and have both regular and misbehaving stone. I cannot confirm if my misbehaving one comes from cooked cobblestone but it is very likely, although it is not systematic. I also have stone from furnaces that behaves normally.