In this paper, we examine the effects of excessive sonication during surfactant-assisted multiwall carbon nanotubes (MWCNT) dispersion in ethylene vinyl acetate (EVA) by way of monitoring molecular arrangements upon progressive straining. Aberration-corrected transmission electron microscopy confirms the structural damage on the graphitic layers upon prolonged sonication. The resulting lack on MWCNT alignment is shown by atomic force microscopy. Further, molecular interface dynamics in progressively strained EVA|MWCNT composites have been studied through Raman and NEXAFS spectroscopies. NEXAFS spectra have identified graphitic amorphization and further C-vacancy rehybridization by way of hydrogen passivation as the damage mechanism to the graphitic structure upon sonication. In this scheme, MWCNTs did not align despite the range of composite strains discussed due to stick and slip dynamics of surrounding EVA. Ultimately, damaged MWCNTs rendered the necessary dispersant π–π interactions suboptimal and insufficient for nanomechanically interlocked polymer–filler interactions. Remarkably, upon large strains, polymer chains are seen to unlatch from the MWCNT and undergo mechanically induced backbone twisting. The possibility of mechanically induced backbone twisting might offer alternative processing routes in photovoltaic systems, where chemically induced conjugated backbone twisting yields increased power conversion efficiency.