By analysing species differences in brain and behaviour, comparative neuroscience & psychology can help to understand the nature and mechanisms of behaviour. The task is enormously complex due to the number of dimensions onto which species can differ. In addition, it is shown here that the approaches, methods and concepts used in these fields contain numerous issues. Many of these issues result from the persistence of misconceptions on the evolution of brain and behaviour; despite increasing evidence that more complex approaches and concepts should be considered. Most of the issues discussed here have been presented in a previous publication (Willemet, 2013(Willemet, , doi: 10.3389/fpsyg.2013.00396) but have not been addressed by recent literature. They are restated here in detail, using as a reference a recent paper resulting from the cooperative work of many researchers in the field (Maclean et al. 2014, doi: 10.1073/pnas.1323533111). The factors responsible for the evolution of brain structure size are reviewed, with particular emphasis on the adjustment effect recently introduced (Willemet, 2015(Willemet, , doi: 10.3389/fnana.2015. The traditional interpretation of the concept of allometry is critically evaluated, and an alternative is discussed. It is also argued that the lack of consideration towards emotional, motivational and attentional factors constitutes a major obstacle to understanding the evolution of behaviour. A dataset on the neuroecology of repertoire size in songbirds is analyzed using the framework discussed here. It is concluded that until the issues detailed here are addressed, progress in our understanding of the evolution of brain and behaviour will be undermined.