There are 2 little piles of turmeric in Flipside which cannot be picked up -- you can hover the cursor over them to see how many bits of turmeric are there, but you cannot click on them to do anything with them (at least *I* can't...).
And in Groddle Forest Junction, near the flat-topped yellow-beige mushroom you can jump onto, there is a package of strawberry seeds half-embedded in the ground, and cannot be picked up.
And in Lower Valley Hollow, I finally found a piggy plot to investigate/sniff/whatever, except it's almost underground and cannot be clicked/acted upon.