I wasn't able to replicate this, but when you press Z on a spot with Elmsbloom you haven't collected, there is no message, you just pick it up. So you might have just pressed Z on each spot twice, not realizing you'd already picked the Elmsbloom from that spot. If you have a save file that shows the issue, I could look at that to see if there really is a bug going on. Either way, thank you for the bug report.