Yeah, citra is for PC. It still can't play XY yet, but it probably will be able to in the future. The game should be played on an actual 3DS; nothing else can play it right now, unfortunately.
It sounds like you have a game update installed. The cia is probably fine; uninstalling the update from system settings should fix the problem.
Sorry about the horrible installation process. Once I'm sure there are no more changes that need to be made to games I'll release a set of xdelta patches to skip the ROM building part, which will cut the whole process down to a few clicks. I would send you a cia link but my upload speed is terrible, it'd take a few days for me to build and upload 10 different cia files with every update.