I started churning milk until I realized that I could have milked the second goat and added it. I clicked away mid-churn to go do so and my first batch vanished from the pot on the spot.

Encountered this issue as well. Also, I accidentally exited the game at one point (used the esc menu to reset item locations, then accidentally clicked exit instead of return), and when I came back in, the cheese that should have been waiting for me from the previous day was gone from the pot.