Yes, it's the bug I'm referring to in this very update haha
I'm sorry this happened to you. It's fixed on the latest version. But the crate won't respawn for people who already was victim to this bug, unfortunately. But don't worry, I'll guide you through on how to get Wormmon anyway.
Download the game again (1.1.2) and load your game normally. Then go to the initial HUB area (if you're not already there). Then go to a space between the Arena's door and the Baihumon statue to the right. Then press up and the game will ask you for a cheat code. Type "Target" (case sensitive and without the quotation marks) and then press Enter. This will unlock the entire bottom row of characters.
Thanks for playing anyway, it means a lot!