The title says it all. I've only seen it happen with the Warped ones, but it probably happens with the Crimson ones as well. It's not that trees from below the ceiling poke through it, they seem to think that the Nether ceiling is just the ground. (You can't dig through the trees to get to the ceiling.) This doesn't happen with any of the Nether foliage, such as the crimson/warped roots.

(The trees on top of the ceiling look pretty cool, though!)