The listing and automatic detection of ontology pitfalls are crucial in ontology engineering. Existing work mainly focused on detecting pitfalls in stand-alone ontologies. Here, we introduce a new categorization of ontology pitfalls: stand-alone ontology pitfalls, pitfalls in versioned ontologies and, pitfalls in ontology networks. We investigate pitfalls in a situation of ontology co-evolution and we provide a systematic categorization of the different cases that could occur during the co-evolution process over two ontology portals: the Linked Open Vocabulary and BioPortal. We also identify 9 candidate pitfalls that may affect versioned ontologies or ontology networks. We evaluate the importance and potential impact of the candidate pitfalls by means of a web-based survey we conducted in the semantic web community. Participants agreed that listing and investigating ontology pitfalls can effectively enhance the quality of ontologies and affect positively the use of ontologies. Moreover, the participants substantially agreed with the new categorization we proposed. We conclude by providing a set of recommendations to avoid or solve the different pitfalls we identified.