Oh autopilot. Autopilot really does suck, but there are ways to circumvent autopilot. Now, I'm not sure how bad your autopilot is since we all think differently, but hopefully, my tips can help you.
One way to avoid autopilot is to focus on your opponent. What I mean by this is to actually watch your opponent. Watching your opponent's character will help you focus on what your opponent is about to do to you. You'll also be more likely to catch on to your opponent's habits when you look at them and you'll be able to react to your opponent a lot more effectively.
Another way that can help is to constantly ask yourself questions while playing. "How and why did I get hit by that combo?" "How did I lose my stock?" "How did my opponent lose their stock?" "What are my opponent's worst habits?" "Am I being too predictable?" Asking yourself questions like those while playing will help you maintain focus while playing since you'll be thinking what you are doing while playing.