Cactus was generated first, two-tall... then tree grew through it... killing the lower part.
Also note... You are in "fast render", which makes leaves "solid blocks", which makes them grow mushrooms on them too. Try planting a tree on some leaves... (Monsters will also spawn on them, as well as critters... if pigs and sheep and cows could fly... that would explain a lot. But it is just changing your graphics mode to "fancy" which turns the blocks back into "transparent-blocks", which limits those odd things.)
Also note... vines are generated first, on some trees, which makes new trees form around the vines, cutting tunnels in the leaves. Looks odd.
Explanation?
Example: Tall grass spawning on dirt blocks
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Also note... You are in "fast render", which makes leaves "solid blocks", which makes them grow mushrooms on them too. Try planting a tree on some leaves... (Monsters will also spawn on them, as well as critters... if pigs and sheep and cows could fly... that would explain a lot. But it is just changing your graphics mode to "fancy" which turns the blocks back into "transparent-blocks", which limits those odd things.)
Also note... vines are generated first, on some trees, which makes new trees form around the vines, cutting tunnels in the leaves. Looks odd.