The middle leaf block is invisible, but the stem itself is not. The modpack I'm playing is Roguelike Adventures and Dungeons (version 1.47a). Functionally the block works the way it's supposed (can be bonemealed) but the texture is missing.

A year later, but I also ran into this issue on Enigmatica 2: Expert. I have run some isolated tests and found that the culprit is the FoamFix mod.

Additional testing and I have found that in the foamfix config this can be fixed by changing

More optimized multipart model condition storage. Inspired by malte0811's research. [default: true]
B:smallModelConditions=true

to

More optimized multipart model condition storage. Inspired by malte0811's research. [default: true]
B:smallModelConditions=false