Attribute that to this program itself. Heal it, put it in the daycare or fix it in PKHeX. This app is notorious for mangling the hex values/trashbytes and those are your only options to fix it. Although, I've never had a problem with cloning anything with this program. They all work fine. I'm going to say something is wrong with your original pokemon. Did you try the other one online? Were you playing ranked?i cloned one and it wasnt legit online, despite the original being wild caught in game with no modifications
Either way it's confirmed if you read a few pages back; clones work fine unless your original is illegal. Genning (more often than not) scrambles data and requires a quick fix as stated above. Otherwise, check it in PKHeX on the PC and see what you can find.