Need help with two fragments- Vanille's Fruit and Fang's Crown- Please read!

I am having alot of trouble with these two fragments. Please read below, as I already know you have to play back through Academia 4XX to get them if you missed them, just please read. I did miss Vanille's Fruit and Fang's Crown fragments the first time, went on, and came back to close the gate to Academia later to get them. Played all the way through Academia, Void Beyond, went through New Bodhum, interacted with Lightning, then Fang and Vanille again. After the scene, I picked up both items and got both fragments before entering the gate again and proceeding to A Dying World, then back to the Historia Crux. While the gate was closed, it said I had collected the two fragments, but when I opened the gate again, the two fragments were not included in my total fragment count, and New Bodhum 700AF still said 3/5 fragments. The fragments seemed to not to have been counted. I couldn't figure out why, thought maybe I forgot to save or something odd, so later, I closed Academia again, replayed all of the stories to Vanille and Fang, and after their scene, looked around again for the items, and they were not there. I searched everywhere, and I have repeated this search twice- The fragments are not there after closing the gate, and they are not included in my fragment total or in the New Bodhum 700AF count, even though I am sure now I got them the first time. Someone please tell me what in the world is going on, have I missed something, messed something up, can I ever beat the game?? All help is appreciated!