Every scientific practice rests on implicit unrevised theoretical assumptions. Neuroscience, in particular, focuses on a very controversial object of study-the brain and is therefore prone to tacitly embrace philosophical positions in its everyday workings. It is thus, of utmost importance, to develop a critique of the structure of neuroscientific investigation so as to understand what the uncovered pillars of the field are, what pitfalls they may implicate and how we can correct them. In this paper, I gather the first critiques in animal cognitive neuroscience and hope to establish the first step in a continuous process of revision. By applying a conceptual division of neuroscience into cognitive, behavioral and neurobiological theories, I point out the main problems in articulating the three, based on actual scientific practice rather than purely theoretical reasoning. I conclude by proposing developments on behavioral theory and set an initial critique on assumptions on both cognitive and neurobiological theories.