You're not alone there, I'm also getting this problem. It's not all the time, either. Pressing CTRL also brings up a battle target while engaged in battle, meaning that I'm missing cures and raises (think PVP here) because a battle target is being brought up from CTRL. Outside of battle, while on the field, this is temperamental at best. 70% of the time CTRL will stop me, then randomly it behaves itself.
Also worth noting is that numpad 0 seems to have stopped bringing up the submenu for targeted PCs, which I use quite a bit too.