Modularization entails more efficient reasoning and better performance in the ontology manipulation process. Therefore, the development of modular ontologies has recently received much attention. One of the most important issues in modular ontologies is dealing with inconsistencies. An inconsistent module may affect the other modules and cause a modular ontology to become inconsistent. Furthermore, the integration of different consistent modules may also result in inconsistency. In this paper, we investigate various types of inconsistencies in modular ontologies. We mostly focus on an interface-based ontology modularity formalism and propose a strategy and an algorithm for isolating inconsistent modules and resolving inconsistencies arisen from the integration of different ontology modules.