Playing on a server with my family we had issues with trees killing our animals and suffocating us, so we decided to build an underground tree farm and have fences next to the tree to keep them higher than the player. They grew through the ceiling of the tree farm which was dirt, turning dirt into logs and killing animals and suffocating players who were on the surface. We are playing in a world with the new world border block and they also grew through that into dirt in the wall. The tree farm room was 8 high not counting ground level, we reinforced the ceiling with cobble in hopes that that would prevent any more tree damage.