We provide two approaches for explaining inconsistency in multi-context systems, where decentralized and heterogeneous system parts interact via nonmonotonic bridge rules. Inconsistencies arise easily in such scenarios, and nonmonotonicity calls for specific methods of inconsistency analysis. Both our approaches characterize inconsistency in terms of involved bridge rules: either by pointing out rules which need to be altered for restoring consistency, or by finding combinations of rules which cause inconsistency. We show duality and modularity properties, give precise complexity characterizations, and provide algorithms for computation using HEXprograms. Our results form a basis for inconsistency management in heterogeneous knowledge integration systems.