Occasionally items are not picked up, even though there is room in inventory. While looking at other tickets, I saw several in various different specific examples, but it's come up at many different times. I see this perhaps once per week or two.

Here's a screenshot of a sapling I could not get. Sometimes digging out the block beneath it makes it work, sometimes not. In this case, I could not get it until I quit and reentered the game. It automatically popped into inventory as soon as the game loaded.