Wood replaces stone

I have an underground tree farm. I have had two trees grow where the top 1-3 blocks of trunk replaced stone blocks in the ceiling. I have included a snapshot of the roof. You can see the two areas where there is stone missing. I don't know if this is related to any other tree issues or not. I have only seen it with oak trees, but that doesn't mean it is exclusive to oak trees. The already rain glitch is visible here too. Thanks for all you do, Luke. AKA, Sacul1990.