Previous work has proposed consistent query answering as a way to resolve inconsistencies in ontologies. In these approaches to consistent query answering, however, only inconsistencies due to errors in the underlying database are considered. In this paper, we additionally assume that ontological axioms may be erroneous, and that some database atoms and ontological axioms may not be removed to resolve inconsistencies. This problem is especially well-suited in debugging mappings between distributed ontologies. We define two different semantics, one where ontological axioms as a whole are ignored to resolve an inconsistency, and one where only some of their instances are ignored. We then give a precise picture of the complexity of consistent query answering under these two semantics when ontological axioms are encoded as different classes of existential rules. In the course of this, we also close two open complexity problems in standard consistent query answering under existential rules.