Yes, indeed, we don't always have conscious control over the same set of things over which we intuitively believe we have conscious control. That's the foundation of (among other things) the difference between System 1 and System 2 in the biases literature. It's also (as Kaj_Sotala noted) one reason habit is such a powerful influence on human behaviour, and the reason things like drug addiction exist. But how could it be any other way? Brains aren't made of magical-consciousness-stuff, they're physical, modular, evolved entities in a species descended from lizards.

I'd be interested in hearing more about the methods you've found effective for noticing the semiconscious decisions that you're making and how you've evaluated their effectiveness.