Hey, I love the game. It's really cute :) I just wanna tell u that while I was playing I found this one entrenched crystal and when I swam up to it, I got the entrenched crystal but it didn't go away so then I swam up to it again and I got another one. I did it three more time and it still didn't go away.
That happened to me, and i found the solution. Your inventory is full. So go back up to the tree, and drop a few crystals (not five. Then it will trigger the next scene) and go back down and you should be able to pick the crystal up.
Of course, that's how I did it, i'm not sure if it will work the same way for you. I hope it does though!