How to reproduce:

1. Grab yourself a piece of bonemeal and find some grass blocks.
2. Use the bone meal on the grass blocks.
3. Go to Statistics > Items and note that the "Times Used" column didn't increase for bone meal (on a fresh server, bone meal won't be present as a row).

I'm thinking this branch is entered: https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/browse/nms-patches/net/minecraft/world/item/ItemStack.patch#121, which prevents the statistic from being granted later down the line: https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/browse/nms-patches/net/minecraft/world/item/ItemStack.patch#248.