The "Lair Herbalism Bowl" feature is not counting the (new) gathered resources such as bottles of tar and fungi toward the tally. I imagine the resulting resources from the newly implemented change just aren't tagged correctly.
Edit: I forgot to mention that guts and sinews are still counted, which leads me to believe the above assessment is true.
Bump'd
Putting vegetation like Amanite into the lair doesn't apply them to the herbalism bowl. At the moment no matter what I add to the lair the bowl doesn't reflect the stored resources, and when clicking to try to craft stuff with the herbalism bowl it always replies "You don't have any supplies".
I haven't tried guts or sinews so I don't know if the above is true.
As far as I've seen, the herbalism bowl doesn't work at all (including guts and sinews). It's a known issue, but I'm not sure where it's at in the list of things.