This page of our guide to Psychonauts 2 lists the Memory Vaults available in Bob's Bottles.
Two Memory Vaults can be found in this level.
Cutting the Root
Location Ship in a Bottle.
That secret is behind closed doors. The only way you can open it is by using Projection power. After opening the door, run inside and attack the Memory Vaults.
Location: Bog of the Betrothed.
This secret is right next to entrance to the purple bottle. All you have to do is turn right, jump onto the white-red ramp, and then run through the tables until you reach a separate room.