New Anomalies in Topological String Theory

We show that the topological string partition function with D-branes on a compact Calabi-Yau manifold has new anomalies that spoil the recursive structure of the holomorphic anomaly equation and introduce dependence on wrong moduli (such as complex structure moduli in the A-model), unless the disk one-point functions vanish. This provides a microscopic explanation for the recent result of Walcher in arXiv:0712.2775 on counting of BPS states in M-theory using the topological string partition function. The relevance of vanishing disk one-point functions to large N duality for compact Calabi-Yau manifolds is noted.