Put the summary of the bug you're having here
What I expected to happen was...:
When a jungle tree was grown from a sapling, I expected it to avoid replacing solid blocks, including walls.
What actually happened was...:
I had the trees in a deep pit surrounded by a mossy cobblestone walkway and mossy cobblestone wall for aesthetics; a segment of the wall at the top was replaced by leaf blocks.
Steps to Reproduce:
1. Plant a jungle or birch tree
2. Place mossy cobblestone (or presumably also cobblestone) wall close to the sapling and above, at leaf-height).
3. Wait for it to grow or use bonemeal.
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Yes. Leaves "destroy" the wall. The wall disappeared

Screenshot
I built wall tower and leaves destroyed it

Confirmed (in creative), before and after screenshots added.

Before applying bonemeal.

After applying bonemeal, multiple wall blocks removed.

EDIT: Sorry, I said I have this problem with Stone Brick blocks, but I was mistaken. It's a problem I'm having with stone brick STAIRS. Stairs placed on a ceiling are overwritten by my birch tree leaves growing.

Confirmed, and this occurs with any block that has transparency.

As MC-147 have been fixed, I guess this has been fixed as well. Is this still a problem in 1.4.4 ?

Duplicate of MC-147.

Not fixed in 1.4.4: wall around the tree was all the same height before bone meal applied to sapling.
As can be seen in screen shot 2012-11-12_16.37.10.png most of the top row of wall has been replaced by the tree.

Re Richard Cox: I am unable to recreate the problem in 1.4.4; when using bonemeal to grow an oak tree, the leaves no longer replace blocks: I have tried this with fence, nether brick fence, mossy cobblestone wall, and glass blocks. Leaves are missing where these blocks obstruct them, or the tree is entirely unable to grow. This is shown in the attached screenshot (tree-obstructed.jpg). The bug appears to have been resolved.

Also unable to reproduce in 1.4.4 with cobblestone wall.

Just tried again Added before and after shots. Note the single wall block on the right front corner with a leaf block below that was wall.
NB. This is using a larch sampling in single player creative.
1.4.4 pre-release.

... and just tried the same with an oak sampling and did not re-create.
So there is a species dependency.

I just tried again and I can confirm that the bug still exists for both jungle trees and birch trees. I also tried oak and pine trees, but neither appeared able to replace mossy cobblestone wall during my attempts. Richard Cox seems to be correct, this only happens for Birch and Jungle trees.

I have uploaded the screenshot birch-replaces-wall.png to demonstrate that birch leaves still replace mossy cobblestone wall as of 1.4.4. The red dots point out the only 3 wall blocks remaining of what was previously a complete square.
This also happens with jungle trees.

Reopening issue, as it seems it is still a problem.

You should update the affected version to 1.4.4

The leaves break stairs too.

It happens in 1.4.5 too.

I have this happen to me with torches all the time. I'll have built a tree farm and I'll put torches around the walls half way up to make sure everything is well lit, and sometimes when the trees grow they replace some of those torches. Tree growing algorithm needs to check the block matrix to see if it says the blocks are anything other than 0, not just something that would let it replace transparent blocks.

@Chad: It probably needs to be a little more complicated (leaves and vines shouldn't probably hinder tree growth for example) but generally I completely agree.

This happened to me with birch and oak stairs/glass blocks in 13w04a

Reopening due to MC-16255. The leaves replacing bonus chests issue still exists.

The leaves still delete the bonus chest in the 1.6 Prerelease. Seed 5482309864025477364 has this happen.

Cannot reproduce in the latest version of minecraft

Here's how to reproduce this on the latest snapshot 15w34a.
Create a new survival world with a bonus chest using seed: -6625871255631194444
Depending on where you spawn, you may pick up the bonus chest contents before the world even finishes generating, but if you don't, they should be scattered around -84, 72, 258, next to two torches which surround one leaf block that apparently destroyed the bonus chest at generation time.
Chests seem like a particularly important block to protect from leaf generation.
I also tested Chris Keohler's seed mentioned above, but with the changes to world generation that seed no longer is affected.

Yup, confirmed in 15w34b.
I couldn't reproduce the birch tree bug as in the description, but the "bonus chest being destroyed in jungles" part is now fixed