I know this thread is a bit out of date but I've been having this issue on my android. I've donated the ancient seed and have the recipe but it still shows up as ??? in my collections tab. I tried deconstructing some seeds and Gunther wouldn't accept it. It's sitting there with all the other stuff I've found at the library. I even got the achievement and star as well as the stardrop. It just also stills says "???" in collection tab.
What I finally discovered after this same thing happening in a whole bunch of games is that (at least on my Android tablet) when you get something in a fishing treasure chest, it is not showing up in your collections tab.
.
One way to get around it is hope to get another one through some other means such as a monster drop or from an artifact spot. One of the things I kept getting from a treasure chest is/was the skeletal tail. I would turn it in at the museum but it never showed on my collections tab. I've learned to use my hoe on the dirt spots in the mines from levels 5 to 29 and I can almost always get another one and that one ends up showing in my collections tab.
I find quite a few ancient seeds when I fight the flying bugs, the crawling grub thingies and scythe the fiber in the Mutant Bug Lair in the sewer so if you have access to that area, maybe try to get another from there.
