Yes. How I normally do tree farms is I make a large 20x20-ish open space of dirt, surround it with glass walls to keep the mobs out, place torches around the perimeter, and leave the top open for room to grow. The trouble is, now bonemeal won't work on the 2x2 jungle trees and they won't grow normally either. I can still plant normal, single-sapling trees, but that's obviously a lot less efficient than full jungle trees. It's something I can work around, but it's getting to be a major annoyance.