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Intentionality is consciousness + directionality as Husserl wrote. It is not simply directed at objects, but is the process of objectification itself. The above means that you are perceiving the pen in your hand, you are creating the object of the pen also, usually defined by higher level features and the function of the pen in relation to other objects such as paper, eraser, and so on. So your consideration of the pen is an approximating. Furthermore, objects withdraw when their function is fulfilled. As you are reading this, you do not consider the wifi router, as the wifi router only appears as an object when it either fails to perform its function, or if you are considering it directly as a higher level phenomenon.
That we sleep, die, and have no access to other minds causes the brain phenomenon to appear to us as object of mind. So we assert the existence of a transcendental mind, unity of apperception, or whatever. Also, as I explained above, considering is objectifying and approximating, so self-reflection is both the establishment of a unity of mind as function, but also an approximating of it as higher level phenomena. Your approximating of your mind can't give you total access to it contents, or its processes. We do not understand how the mind machine works on a detailed level.
So that is what is happening to you. The consciousness is an approximating and objectification, so the intent of intentionality is itself created as object as an approximating of the complexity of your neural processes. There are not two distinct strata of conscious and unconscious in conflict, they are the same processes, but consciousness is the approximating of the functions of the brain machine.... a sort of GUI.
You are aware of the brain machine because it is failing to complete its function of approximating what it most prefers. What you are experiencing is guilt about your true preferences not reflecting your expected / approximated preferences.