I originally thought it was my eyes playing a trick on me, but when I craft some of the compost bins and place them in the world and after I am done playing, I shut down MC, and the compost bins disappear upon relaunch and reload of MC.

It doesn't occur 100% of the time (upon doing some testing on my own), and I tested with the mod by itself and it would occur sometimes.

i also get this bug

This bug happened to me too. Although I thought maybe it was because the crate's output was almost (55 items) and I added more items to decompose.