We study the effect of Active Nuclei Galaxy (AGN) feedback as one of the major mechanisms modifying the cluster morphology influencing scaling relations, which are the most uncertain factor in constraining cosmology with clusters of galaxies. Using cosmological hydrodynamical simulations we investigate how the AGN feedback changes the X-ray morphology of the simulated systems, and compare to the observed REXCESS (Representative XMM-Newton Cluster Structure Survey) clusters. We apply centre shifts and power ratios to characterise the cluster morphology, and find that our simulated clusters are more substructured than the observed ones. We show that the degree of this discrepancy is affected by the inclusion of AGN feedback. While the clusters simulated with the AGN feedback are in much better agreement with the REXCESS L_X-T relation, they are also more substructured, which increases the tension with observations. This suggests that not only global cluster properties such as L_X and T and radial profiles should be used to compare and to calibrate simulations with observations, but also substructure measures such as centre shifts and power ratios. We discuss what changes in the simulations might ease the tension with observational constraints on these quantities.