That actually is a special hacked item called the "infinity gift wrapped gift" from before the update and not a glitch but not sure from which hacking program/modification program it was from. If he picked it up at anytime in a dream town or had someone over who left it there I don't know how a special made hacked item like that would end up on a non hacked town. It is in no way a glitch and most who follow this stuff know about the "infinity gift wrapped gift". However, I can say no matter how they got it, it would not necessarily be the cause of the issue of not being able to play the game. Virtually all hacked items are/were transported safely into the new update. They patched only a few methods of how you can hack, however, just a few weeks ago a new hack method came out so all of that patching was kinda pointless to do. I know all of this not because I do it personally but because I search the internet frequently on hacking the new update. There are actually 2 welcome amiibo updates and with each one it has to update BOTH your cartridge and your system. There was the initial update and then I believe a few days later another update happened. I have all my carts updated only to the first one. It could be that your game is glitching between the two updates not knowing which one to use if one part was updated only once but the other was updated both times. It doesn't know which one to use. This issue was stated to happen with the initial update but the reverse action would happen-if you installed the update but then delated it, since the update effects both the cartridge and system, once uninstalled from one but not the other you would not be able to play the game and would need to reinstall the update both times.
It sounds like your game and your system is not installing and unistalling BOTH updates for both game and system. Unless you take it in or are able to scan your system and your game individually yourself and completely remove every file from both updates and then reinstall both to both game and system not much you will be able to do. I hope I have explained it well.
Most people don't know of the second update that happened because it wasn't widely announced. It was only made known that there was an update, not how many there were. If I could take screen shots of what I mean by have both updates I would. My game shows up with the first amiibo update screen splashed across my screen but when I go to play it says a another new update is available. I have two options that come up Y.launch or I think A.install update. I always chose Y.launch. I don't want to install the second update as I am too afraid I might wind up with same problem as you.
And soooo damn sorry for being long winded. Really hard to explain all this without being.