Yeah, I had a similar problem back on Red/Blue. I'd traded the 3 starters onto one cart, so I had all three to begin with. Working through, by about L12 onwards the two that were traded were disobeying me, doing different moves or just ignoring me altogether.
Once you have a Gym Badge that matches their level, they started obeying me again. Although, I was careful to slow down their levelling until the next gym, in case they went too high. The traded 1.5 x Exp bonus does help in levelling, but can be a double edged sword if they level too quickly