The tree leaves in your graveyards are set to persistent, this means that they will never decay even when you have broken all the wood, leaving the leaves floating forever unless the player breaks them.

This is true of all the structures in version 1.4 (latest release on curseforge as of posting this issue) except mushroom grave and small grave as they do not have any trees in them.

Well this isn't bug. All trees are custom, so the leaves must be persistent or else they will despawn, because most of the graveyard trees do not follow the "4 blocks away from log"-rule from minecraft.
Or I'd need to adjust the graveyard trees to match that rule, but then the trees wouldn't look as good.

iirc generated structure leaves wont start following this unless they get a block update, is this not the case?

I'm pretty sure the leaf block itself is ticking and checking if it is close enough to logs.
And it seems the distance is 7 and not 4 - so maybe it could work out. I'll need to do some testing on this one

they do actually decay in generated structures, i guess thats been changed at some point :/

however, setting the distance value to <7 will make them all stay, until they recieve a block update, anyway. In my lil test some of the cocoa beans broke the tallest tree in the desert graveyard. the mechanic is kinda jank but atleast some of the leaves decay? i guess, lol.

however it also seems like leaves dont send updates on diagonals, and removing diagonals would change the look of a lot of the trees quite a bit. mega rip

i would like to note though, with some trees such as (all the ones i checked) spruce trees in the large walled graveyard dont need persistence as none of them reach the distance cap of 7

Thanks a lot for checking that. I'll look that i'll change that for the next update!

Fixed in 1.9. Took a bit longer than expected and definitely not the most fun activity, but...