I will answer this in the context of OWL ontologies where the errors are found using Hermit or Fact++ as the inference engine. I happen to use Protégé, but other ontology tools have similar functionality. There are a few cases. First, if the ontology is inconsistent, then one or more classes will be inferred to be equivalent to owl:Nothing and will show in red in the inferred class hierarchy. Click on one of those classes and click the question mark to get the explanation for that inference. Scan the explanation to see if you can find anything obvious. Much of the time, you will see that a property is used in a restriction instead of its inverse. If nothing is obvious, consider what you changed most recently in the ontology, and look there. If you still cannot find the problem, try clicking on other classes that are equivalent to owl:Nothing to see if there are any shorter explanations that may be easier to track down. If they all are approximately the same length, then you might just have to roll up your shirtsleeves and draw some venn diagrams or graphs connecting classes and properties to identify the problem.
After the ontology is consistent, there might still be some classes inferred equivalent to owl:Nothing. Use the same procedure as above. After this, look carefully at the whole of the inferred hierarchy to identify things that do not look correct. Find the explanation and proceed as before.