I can suggest a few things.
First, did you use the legality checker to see if the Pokemon are actually legit? Or do they just look legit? Even if you didn't use the legality checker, if you gave them reasonable IV's, EV's, and moves for their levels, it shouldn't be an issue. Also make sure that you made them caught at their actual locations. Otherwise you can forget it.
Second. Why don't you just catch the Pokemon in the game? Unless you already defeated them..you should be able to catch them and then you shouldn't have to deal with the legality of them. If you did beat them, try to get them off of WiFi if the one's you're making don't work right.
Third. Are you using any other Pokemon that are questionable at the same time? If you're positive that you made the three in question legit, then make sure that the rest of the Pokemon on your team (if they're PokeSav'ed) are legit as well.
Hope I could help.
Want a Pokemon code? Feel free to message me, I'll be glad to try and help you!