Recent publications have reported the presence of hexagonal phases in Si nanowires. Most of these reports were based on 'odd' diffraction patterns and HRTEM images - 'odd' means that these images and diffraction patterns could not be obtained on perfect silicon crystals in the classical diamond cubic structure. We analyze the origin of these 'odd' patterns and images by studying the case of various Si nanowires grown using either Ni or Au as catalysts in combination with P or Al doping. Two models could explain the experimental results: (i)the presence of a hexagonal phase or (ii)the presence of defects that we call 'hidden' defects because they cannot be directly observed in most images. We show that in many cases one direction of observation is not sufficient to distinguish between the two models. Several directions of observations have to be used. Secondly, conventional TEM images, i.e.bright-field two-beam and dark-field images, are of great value in the identification of 'hidden' defects. In addition, slices of nanowires perpendicular to the growth axis can be very useful. In the studied nanowires no hexagonal phase with long range order is found and the 'odd' images and diffraction patterns are mostly due to planar defects causing superposition of different crystal grains. Finally, we show that in Raman experiments the defect-rich NWs can give rise to a Raman peak shifted to 504-511cm - 1 with respect to the Si bulk peak at 520cm - 1, indicating that Raman cannot be used to identify a hexagonal phase.