We analyze the Wald entropy for different forms of the conformal anomaly in six dimensions. In particular we focus on the anomaly which arises in a holographic calculation of Henningson and Skenderis. The various presentations of the anomaly differ by some total derivative terms. We calculate the corresponding Wald entropy for surfaces which do not have an Abelian O(2) symmetry in the transverse direction although the extrinsic curvature vanishes. We demonstrate that for this class of surfaces the Wald entropy is different for different forms of the conformal anomaly. The difference is due to the total derivative terms which are present in the anomaly. We analyze the conformal invariance of the Wald entropy for the holographic conformal anomaly and demonstrate that the violation of the invariance is due to the contributions of the total derivative terms in the anomaly. Finally, we make more precise general form of the Hung-Myers-Smolkin discrepancy.