I've been using a cow with plant growth boost for a few days, and today, after harvesting some plants, it simply forgot to boost some of them.
After the lychees and passion fruit grew, the boost count returned to normal, but they weren't actually gaining the time boost. I'll check if this bug happens again when I remove a lot of things from the garden.
(I had 19 plants growing and the boost activated for 13. In the image, I have 16 plants growing and only 12 received the boost)