My first experience with this happened with my Luxray. Luxray was on of my best Pokemon in Pearl. After beating the game, I used an action replay to get rare candies to level up Luxray to lv.100 and to by the super expensive ribbons for it. Later, i traded it over to Platinum and I didn't pay attention/know about pokemon not listening to you if you didn't have the right amount of badges. It crushed my heart, because I thought that Luxray hated me for using cheats / the game realized I had cheated and was punishing me (I was younger, and thought that way at the time. Games were more real than coded information to me.)
I've never really used Luxray again and I've lost a certain connection towards it. I still transferred it over to Alpha Sapphire and hope to use it more in the future, after all, Luxray was my best and favorite Pokemon back in Pearl.