Lava and water won't create cobblestone if the lava has already flowed completely.
Steps to reproduce:
1 - Place a lava source block;
2 - Let it flow completely;
3 - Place a water source block anywhere near the lava flow;
4 - Cobblestone won't be generated as it should.
In the pictures, a redstone block represents the position of a lava or water source block.
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However, this issue is a Duplicate of MC-4641.
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