I might be missing something since I still haven't bothered finishing the game, but I believe that's on purpose, a representation of your condition's progress with the implication that the construct is well along the way into supplanting the protagonist. When you relinquish control, Johnny takes over, so the first time you're watching him do his shit as an NPC, outside of the player's control. But as you do it more and more, Johnny's subsuming V and slowly being elevated to the status of PC, thus moving him into the player's sphere of control.The writing of the main story is also very inconsistent. For example, you have the option to hand over control of your body at certain points in the story. When this happens for the first time, you’ll only see a super cut of what happened until you regain control. However, later in the story you keep control in this situation and can even make story decisions in them which make absolutely no sense.
This is also reflected in your journal, which is presented in the second person as the voice V might be "hearing" inside of their head. When you start out, that voice is Jackie's, but as you progress, the Spanish terms of endearment peter out and by the third chapter it's all Johnny.
I thought this aspect was well handled, actually.
If this was their intention then they did a poor job of presenting it. You first hand over control during the "Chippin' In" side quest where you'll see the super cut. This leads to the next side quest "Blistering Love" where you already have direct control over Johnny and this happens within two ingame days. There is no gradual build up, no comment from V that he now sees more when Johnny is in charge, nothing. Also, if V is your character, should you even be able to play Johnny at all? Him taking over control should lead to less control instead of more. Given the state of the game it is hard to be sure.