In this paper, a comprehensive analysis on the local electrodynamics at micron level for the second generation of magnetically anisotropic high temperature superconducting (2G-HTS) pancake coils is presented. Special attention has been paid to the influence of prospective winding misalignment factors onto macroscopical quantities such as the hysteresis losses and critical current density inside each turns of a generic 2G-HTS coil, and their relation with the magneto-angular dependence of the infield critical current density J c (B, θ) of the 2G-HTS tape. It has been shown that for low amplitudes of the applied transport current, I I 0.2 a c 0 , the flux-front profile for perfectly aligned pancake coils develops a well-shaped flux-free core with a complete absence of magnetization currents in ∼30% the middle turns, that are enclosed by transport current profiles in similar fashion to what would be observed in superconducting bulks, but with the outer turns showing a clear dominance of magnetization currents. However, the misaligned pancake coils show a notorious deflection of the flux-front semi-elliptical vertices which induces a repositioning of the co-vertices, shaping then a 'worm-like' flux-front profile that is caused by the breakdown in the ordinal symmetry of the mutual inductances. This phenomenon leads to an increment in the Lorentz force between the transport and magnetization currents, what causes an additional source of hysteretic losses which cannot be accounted by classical changes in the size of the flux-front profile. Thus, we have obtained that for relatively large deformations of the pancake coil, up to a 19% increment in the AC losses can be achieved for moderate to low intensities of I a , whilst for currents greater than 0.7I c0 , a striking although low reduction on the AC losses can be achieved, whose main physical signature has been connected to the actual disappearance of the flux-free core inside the superconducting coil.