The KH Wiki states the trinity archives are updated when you play through the ending to clear or reclear an episode of the game. After getting all the items, did you clear the ending again with all characters? If not, that could be the reason.
If you cleared them and you're still at 99%, don't give up, there must be a reason.
For Terra, Aqua and Ven episodes you have all commands for every character, right? You have completed the command section of each journal.
It has to be an item which is not a command. It's not an ice cream because you would already know. If there is any item or optional keyblade that you got for just one or two characters, try to get it for the three of them. The optional keyblades are Victory Line, Ultima Weapon, Sweetstack, Void Gear, No Name and Crown Unlimit.
Go to the Mirage Arena and check if you have bought all items, specially the tickets that unlock battles. They're not mandatory as the battles are unlocked when you reach certain Mirage Arena levels, but you must buy them because they count towards item completion. There are 6 tickets: Risky Ticket, Sentinel Ticket, Ringer Ticket, Threat Ticket, Treasure Ticket and Chill Ticket.
Check if you have all synthesis crystals for each character as well. It's highly unlikely (I'd say impossible) that you missed one, but who knows.
There aren't many items in the game which are not in the commands section, it should be relatively easy to find out.