JEI shows the crafting recipe for the bonsai pot but does not show any of the uses. For example, it does not show that an apple can come from the bonsai.

BonsaiTrees: 3.1.0
Libnonymous: 2.1.0
JEI: 1.18.2-9.7.0.192
Forge: 40.0.52

Update: I created a test world with only the mods listed above, and did not see any issues. The problem must be an unexplained interaction from some other mod.