OK, I'll share the rumors I've heard. For example, there was a rumor about a guy cloning his Zygardes with MegaStones, and sending them to random people on the GTS who were giving out Growlithes and Vulpixes, so someone thought the Zygarde he ''received'' was a glitch and posted a Video on YouTube named ''The GTS Zygarde Glitch'' even though it's fake, because I never received a Zygarde for a Growlithe or Vulpix (BTW, both his Vulpix and Zygarde had the same OT and Trainer ID, so, yeah...FAKE....) Video got removed for some unknown reason.
Another rumor about cloning was cloning Pokemon/Items via changing SD cards and copying the files, but the guy who made the video did a MAJOR mistake, so everyone knew it was phony (he took out the SD card out of the 3DS and dropped it on the floor. Then, he took the SD card that was to his left when he dropped the first one on his RIGHT) Tested it, not working at all... But how he winded up with 3 or 4 Yveltals with the same nature, same stats, etc... at the end of his video is a mystery.
...I was thinking these dudes were trying to hide the REAL way to clone Pokemon in X/Y, while other people said the 1.2 Patch would erase the Pokemon rather than cloning it, but I do not know if it is true or not, though.